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changeset 15:bf28a8cff401 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 2f6456c314c010fd73f5eeaf809a9afce47353af
author bgruening
date Wed, 20 Mar 2024 07:34:52 +0000
parents 6f28e90db932
children
files macros.xml mafft-add.xml mafft.xml test-data/mafft_auto_linsi.aln test-data/mafft_custom_original.clustal.aln test-data/mafft_custom_parttree.aln test-data/mafft_custom_result.aln test-data/mafft_default.aln test-data/mafft_explicit_amino_blosum80.clustal.aln test-data/mafft_fftns_result.aln test-data/mafft_kimura40.phylip.aln test-data/mafft_nwns_result.aln test-data/sample.fa test-data/sample_amino.fa test-data/sample_nuc.fa
diffstat 15 files changed, 3444 insertions(+), 2000 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Oct 31 15:48:53 2023 +0000
+++ b/macros.xml	Wed Mar 20 07:34:52 2024 +0000
@@ -1,22 +1,55 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">7.508</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">7.520</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
+    <!-- currently, the fasta3 executable is named according to its major version
+    => needs updating together with the package requirement! -->
+    <token name="@FASTA3_EXEC@">fasta36</token>
     <xml name="biotools">
         <xrefs>
             <xref type="bio.tools">MAFFT</xref>
         </xrefs>
     </xml>
     <xml name="requirements">
-      <requirements>
-          <requirement type="package" version="@TOOL_VERSION@">mafft</requirement>
-          <requirement type="package" version="36.3.8">fasta3</requirement>
-      </requirements>
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">mafft</requirement>
+            <requirement type="package" version="36.3.8">fasta3</requirement>
+        </requirements>
+    </xml>
+    <xml name="weighti_param">
+        <param argument="--weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments."/>
+    </xml>
+    <xml name="parttree_parameters">
+        <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is built this number of times in the progressive stage."/>
+        <param argument="--partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm."/>
+        <param argument="--groupsize" type="integer" value="-1" min="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/>
+    </xml>
+    <xml name="misc_scoring_scheme">
+        <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?" />
+        <conditional name="gap_costs">
+            <param name="use_defaults" type="select" label="Configure gap costs">
+                <option value="yes">Use default values</option>
+                <option value="no">Set values</option>
+            </param>
+            <when value="yes"/>
+            <when value="no">
+                <param argument="--ep" type="float" value="0.0" label="Gap extension penalty for group-to-group alignment" help="Offset value, which works like gap extension penalty, for group-to-group alignment."/>
+                <param argument="--op" type="float" value="1.53" label="Gap opening penalty at group-to-group alignment." help="1.53 default value"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="global_align_options">
+        <section name="treat_unrelated_segments" title="Handling of unrelated segments in global alignments" expanded="true">
+            <param argument="--unalignlevel" type="float" min="0" max="0.8" value="0" label="Over-alignment correction factor" help="The higher this factor the more likely will unrelated sequence stretches in globally related sequences be left unaligned. The default of 0 turns over-alignment correction off, turning it on increases run time."/>
+            <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for > ~1000 sequences."/>
+        </section>
     </xml>
     <xml name="citations">
-      <citations>
-          <citation type="doi">10.1093/molbev/mst010</citation>
-      </citations>
+        <citations>
+            <citation type="doi">10.1093/nar/gkf436</citation>
+            <citation type="doi">10.1093/nar/gki198</citation>
+            <citation type="doi">10.1093/molbev/mst010</citation>
+        </citations>
     </xml>
 </macros>
--- a/mafft-add.xml	Tue Oct 31 15:48:53 2023 +0000
+++ b/mafft-add.xml	Wed Mar 20 07:34:52 2024 +0000
@@ -16,43 +16,53 @@
   </version_command>
   <command>
     <![CDATA[
+      sh mk_symlinks.sh &&
       mafft
       #if $sequences.sequenceType == 'singleseq'
-        $sequences.preservegap  '$inputSequences'
+        $sequences.preservegap input_dir/sequence
       #elif $sequences.sequenceType == 'frags'
-        --addfragments '$inputSequences'
+        --addfragments input_dir/sequence
       #elif $sequences.sequenceType == 'group'
-        --addprofile '$inputSequences'
+        --addprofile input_dir/sequence
       #end if
-      $keeplength $map $reorder
-      '$inputAlignment'
-      > '$outputAlignment'
-      #if $map == '--mapout'
-        && mv '${inputSequences}.map' '$outputmap'
+      $keeplength 
+      $mapout 
+      $reorder
+      input_dir/alignment > '$outputAlignment'
+      
+      #if $mapout
+        && mv input_dir/sequence.map '$outputmap'
       #end if
     ]]>
   </command>
+  <configfiles>
+    <configfile filename="mk_symlinks.sh"><![CDATA[
+mkdir input_dir &&  
+ln -s '$inputSequences' input_dir/sequence &&
+ln -s '$inputAlignment' input_dir/alignment
+    ]]></configfile>
+  </configfiles>
   <inputs>
     <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/>
     <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/>
     <conditional name="sequences">
-      <param name="sequenceType" type="select" label="What do you want to add to the alignment" >
+      <param name="sequenceType" type="select" label="What do you want to add to the alignment?" >
         <option value="singleseq">A single sequence</option>
         <option value="frags" selected="true">Fragments</option>
         <option value="group">An alignment</option>
       </param>
       <when value='singleseq'>
-        <param name="preservegap" type="select" label="Preserve the original alignment" help="Keep the given alignment unchanged (--add .)If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved (--seed)">
-          <option value="--add" selected="true" >Yes</option>
-          <option value="--seed">no</option>
+        <param name="preservegap" type="select" label="Preserve the original alignment." help="Keep the given alignment unchanged .If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved.">
+          <option value="--add" selected="true" >Yes (--add)</option>
+          <option value="--seed">No (--seed)</option>
         </param>
       </when>
       <when value='frags'/>
       <when value='group'/>
     </conditional>
-    <param name="keeplength" type="boolean" truevalue="--keeplength" falsevalue="" checked="True" label="Keep alignment length" help="The alignment length is unchanged.  Insertions at the additional sequences are deleted" />
-    <param name="map" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of positions (--mapout)" help="Output a correspondence table of positions, sequence.map, between before and after the calculation.  The --mapout option automatically turns on the --keeplength option, to keep the numbering of sites in the reference alignment" />
-    <param name="reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences (--reorder)"  />
+    <param argument="--keeplength" type="boolean" truevalue="--keeplength" falsevalue="" checked="True" label="Keep alignment length" help="The alignment length is unchanged.  Insertions at the additional sequences are deleted" />
+    <param argument="--mapout" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of position." help="Output a correspondence table of positions, sequence.map, between before and after the calculation.  The mapout option automatically turns on the keeplength option, to keep the numbering of sites in the reference alignment" />
+    <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences."  />
   </inputs>
   <outputs>
     <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/>
@@ -63,11 +73,11 @@
   <tests>
     <test expect_num_outputs="1" >
       <param name="inputSequences" value="add_seq.fa"/>
-      <param name="inputAlignment" value="mafft_fftns_result.aln"/>
+      <param name="inputAlignment" value="mafft_default.aln"/>
       <param name="sequenceType" value="singleseq"/>
       <param name="preservegap" value="--add"/>
       <param name="keeplength" value="--keeplength"/>
-      <param name="map" value=""/>
+      <param name="mapout" value=""/>
       <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
     </test>
   </tests>
--- a/mafft.xml	Tue Oct 31 15:48:53 2023 +0000
+++ b/mafft.xml	Wed Mar 20 07:34:52 2024 +0000
@@ -1,305 +1,542 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-<description>Multiple alignment program for amino acid or nucleotide sequences</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="biotools"/>
-  <expand macro="requirements" />
-  <stdio>
-    <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-    <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-  </stdio>
-  <version_command>    <![CDATA[
-    mafft --version
-    ]]>
-  </version_command>
-  <command>
-    <![CDATA[
-
-      #if $cond_flavour.flavourType == 'custom'
-        #if $cond_flavour.dist_flavour.distance_method == '--fastapair'
-          export FASTA_4_MAFFT=`which fasta36`;
-        #end if
-      #end if
-
-      #if $cond_flavour.flavourType != 'custom'
-        $cond_flavour.flavourType
-      #elif $cond_flavour.flavourType == 'custom'
-        ### full parameter options
-        mafft
-        $cond_flavour.dist_flavour.distance_method
-        #if $cond_flavour.dist_flavour.distance_method == '--6merpair'
-          --retree $cond_flavour.dist_flavour.retree
-          $cond_flavour.dist_flavour.distance_method.usetree.parttree
-
-          #if $cond_flavour.dist_flavour.distance_method.usetree.parttree==--parttree
-            $cond_flavour.dist_flavour.distance_method.usetree.treedistance
-            $cond_flavour.dist_flavour.distance_method.usetree.partsize
-            $cond_flavour.dist_flavour.distance_method.usetree.groupsize
-          #end if
-
-        #elif $cond_flavour.dist_flavour.distance_method == '--globalpair'
-          --weighti $cond_flavour.dist_flavour.weighti
-        #elif $cond_flavour.dist_flavour.distance_method == '--localpair'
-          --weighti $cond_flavour.dist_flavour.weighti
-          --lop $cond_flavour.dist_flavour.lop
-          --lep $cond_flavour.dist_flavour.lep
-          --lexp $cond_flavour.dist_flavour.lexp
-        #elif $cond_flavour.dist_flavour.distance_method == '--genafpair'
-          --weighti $cond_flavour.dist_flavour.weighti
-          --lop $cond_flavour.dist_flavour.lop
-          --lep $cond_flavour.dist_flavour.lep
-          --lexp $cond_flavour.dist_flavour.lexp
-          --LOP $cond_flavour.dist_flavour.skipLOP
-          --EXP $cond_flavour.dist_flavour.skipEXP 1
-        #elif $cond_flavour.dist_flavour.distance_method == '--fastapair'
-          --weighti $cond_flavour.dist_flavour.weighti
-        #end if
-        --maxiterate $cond_flavour.iterations
-        $cond_flavour.fft
-        $cond_flavour.score
-      #end if
-
-      ## specify threads to use
-      --thread \${GALAXY_SLOTS:-1}
-      $datatype
-      --ep $ep
-      --op $op
-
-      #if $matrix_condition.matrix == "BLOSUM"
-        --bl $matrix_condition.BLOSUM
-      #elif $matrix_condition.matrix == "PAM"
-        --jtt $matrix_condition.PAM
-        --tm $matrix_condition.tm
-      #elif $matrix_condition.matrix == "custom"
-        --aamatrix  '$matrix_condition.matrixfile'
-        --fmodel $matrix_condition.fmodel
-      #end if
-
-      $reorder
-      $getTree
-      $outputFormat
-      '$inputSequences' > '$outputAlignment';
-
-      #if $getTree == "--treeout"
-        mv '${inputSequences}.tree' '$outputTree';
-      #end if
-    ]]>
-  </command>
-  <inputs>
-    <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
-    <param name="datatype" type="select" label="Data type">
-      <option value="">Auto detection</option>
-      <option value="--nuc">Nucleic acids</option>
-      <option value="--amino">Amino acids</option>
-    </param>
-    <conditional name="cond_flavour">
-      <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
-        <option value="mafft --auto">auto</option>
-        <option value="mafft-fftns" selected="true">fftns</option>
-        <option value="mafft-fftnsi">fftnsi</option>
-        <option value="mafft-nwns">nwns</option>
-        <option value="mafft-nwnsi">nwnsi</option>
-        <option value="mafft-einsi">einsi</option>
-        <option value="mafft-ginsi">ginsi</option>
-        <option value="mafft-linsi">linsi</option>
-        <option value="mafft-qinsi">qinsi</option>
-        <option value="mafft-xinsi">xinsi</option>
-        <option value="custom">Custom Parameters</option>
-      </param>
-      <when value="mafft-fftns"/>
-      <when value="mafft --auto"/>
-      <when value="mafft-fftnsi"/>
-      <when value="mafft-nwns"/>
-      <when value="mafft-nwnsi"/>
-      <when value="mafft-einsi"/>
-      <when value="mafft-ginsi"/>
-      <when value="mafft-linsi"/>
-      <when value="mafft-qinsi"/>
-      <when value="mafft-xinsi"/>
-      <when value="custom">
-        <conditional name="dist_flavour">
-          <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
-            <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option>
-            <option value="--globalpair">Global alignment (Needleman-Wunsch)</option>
-            <option value="--localpair">Local alignment (Smith-Waterman)</option>
-            <option value="--genafpair">Local, affine gap cost</option>
-            <option value="--fastapair">All pairwise alignments are computed with FASTA</option>
-          </param>
-          <when value="--6merpair">
-            <param name="retree" type="integer" value="2" min="1" max="100" label="Guide tree is built this number of times in the progressive stage." help="Valid with 6mer distance" />
-            <conditional name="usetree">
-              <param name="parttree" type="select" label="Use a fast tree-building method?" help="Recommended for a large number (> ~10,000) of sequences are input" >
-                <option value="--parttree" selected="true">Yes</option>
-                <option value="">No</option>
-              </param>
-              <when value="--parttree">
-                <param name="treedistance" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
-                  <option value="--fastaparttree" selected="true">Distances based on FASTA</option>
-                  <option value="--dpparttree">Distances based on DP. (Needleman-Wunsch)</option>
-                </param>
-                <param name="partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm" />
-                <param name="groupsize" type="integer" value="" min="0" max="1000" label="Do not make alignment larger than ... sequences" />
-              </when>
-              <when value=""/>
-            </conditional>
-          </when>
-          <when value="--globalpair">
-            <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
-          </when>
-          <when value="--localpair">
-            <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
-            <param name="lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
-            <param name="lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
-            <param name="lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
-          </when>
-          <when value="--genafpair">
-            <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
-            <param name="lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
-            <param name="lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
-            <param name="lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
-            <param name="skipLOP" type="float" value="-6.00" label="Gap opening penalty to skip the alignment" help="-6.00 default value" />
-            <param name="skipEXP" type="float" value="0.00" label="Gap extension penalty to skip the alignment" help="0 default value" />
-          </when>
-          <when value="--fastapair">
-            <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
-          </when>
-        </conditional>
-        <param name="iterations" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
-        <param name="fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
-        <param name="score" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
-      </when>
-    </conditional>
-    <param name="ep" type="float" value="0.0" label="Gap extend penalty for group-to-group alignment" help="Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps" />
-    <param name="op" type="float" value="1.53" label="Gap opening penalty at group-to-group alignment." help="1.53 default value" />
-    <conditional name="matrix_condition">
-      <param name="matrix" type="select" label="Matrix selection" display="radio" help="Usefull only for amino acids" >
-        <option value="">No matrix</option>
-        <option value="BLOSUM" selected="true">BLOSUM</option>
-        <option value="PAM">PAM</option>
-        <option value="custom">Custom</option>
-      </param>
-      <when value=""/>
-      <when value="BLOSUM">
-        <param name="BLOSUM" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
-          <option value="30">30</option>
-          <option value="45">45</option>
-          <option value="62" selected="true">62</option>
-          <option value="80">80</option>
-        </param>
-      </when>
-      <when value="PAM">
-        <param name="PAM" type="integer" value="80" min="1" max="350" label="Coefficient of the JTT PAM matrix" />
-        <param name="tm" type="integer" value="80" min="1" max="350" label="Coefficient of the  transmembrane PAM matrix" />
-      </when>
-      <when value="custom">
-        <param name="matrixfile" type="data" format="txt" label="User-defined AA scoring matrix" help="The format of matrixfile is the same to that of BLAST. Ignored when nucleotide sequences are input."/>
-        <param name="fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition information into the scoring matrix?" />
-      </when>
-    </conditional>
-    <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" />
-    <param name="getTree" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Display alignment tree ?" />
-    <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
-      <option value="" selected="true">FASTA</option>
-      <option value="--clustalout">ClustalW</option>
-      <option value="--phylipout">Phylip</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
-      <change_format>
-        <when input="outputFormat" value="--clustalout" format="clustal"/>
-        <when input="outputFormat" value="--phylipout" format="phylip"/>
-      </change_format>
-    </data>
-    <data name="outputTree" format="txt" label="${tool.name} Guide Tree">
-      <filter>getTree == True</filter>
-    </data>
-  </outputs>
-  <tests>
-    <test expect_num_outputs="1" >
-      <param name="inputSequences" value="sample.fa"/>
-      <param name="flavourType" value="mafft-fftns"/>
-      <param name="outputFormat" value=""/>
-      <output name="outputAlignment" ftype="fasta" file="mafft_fftns_result.aln"/>
-    </test>
-    <test expect_num_outputs="1" >
-      <param name="inputSequences" value="sample.fa"/>
-      <param name="flavourType" value="mafft-nwns"/>
-      <param name="outputFormat" value="--clustalout"/>
-      <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln" lines_diff="2" />
-    </test>
-    <!-- WARNING: the results of the following test depends on #threads.
-    The result seems deterministic for single threaded execution, i.e. GALAXY_SLOTS=1 planemo test
-    However, GH CI/CD uses 2 threads and results vary -->
-    <test expect_num_outputs="1" >
-      <param name="inputSequences" value="sample.fa"/>
-      <param name="flavourType" value="custom"/>
-      <conditional name="matrix_condition">
-        <param name="matrix" value="BLOSUM"/>
-      </conditional>
-      <param name="BLOSUM" value="62"/>
-      <param name="distance_method" value="--fastapair"/>
-      <param name="weighti" value="2.7"/>
-      <param name="iterations" value="1000"/>
-      <param name="outputFormat" value="--clustalout"/>
-      <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln" compare="sim_size">
-        <assert_contents>
-          <has_n_lines n="458" delta="0"/>
-          <has_text text="CLUSTAL format alignment by MAFFT F-INS-i"/>
-          <has_text text="NPIVYGISHPKY"/>
-          <has_text text="1=="/>
-          <has_text text="36=="/>
-          <has_line line="8=opsin,        ------------------------------------------------------------"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help>    <![CDATA[
-      **What it does**
-
-      MAFFT is a multiple sequence alignment program for unix-like operating systems.
-      It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
-      FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
-      From the MAFFT man page, an overview of the different predefined flavours of the tool is as follows:
-
-      **Accuracy-oriented methods:**
-
-      - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
-      - mafft --localpair --maxiterate 1000 input [> output]
-      - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
-      - mafft --globalpair --maxiterate 1000 input [> output]
-      - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
-      - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
-
-      **Speed-oriented methods:**
-
-      - FFT-NS-i (iterative refinement method; two cycles only):
-      - mafft --retree 2 --maxiterate 2 input [> output]
-      - FFT-NS-i (iterative refinement method; max. 1000 iterations):
-      - mafft --retree 2 --maxiterate 1000 input [> output]
-      - FFT-NS-2 (fast; progressive method):
-      - mafft --retree 2 --maxiterate 0 input [> output]
-      - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
-      - mafft --retree 1 --maxiterate 0 input [> output]
-      - NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
-      - mafft --retree 2 --maxiterate 2 --nofft input [> output]
-      - NW-NS-2 (fast; progressive method without the FFT approximation):
-      - mafft --retree 2 --maxiterate 0 --nofft input [> output]
-      - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
-      - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
-
-      **Options:**
-
-      - --auto Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
-      - --adjustdirection Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
-      - --op Gap opening penalty, default: 1.53
-      - --ep Offset (works like gap extension penalty), default: 0.0
-      - --maxiterate Maximum number of iterative refinement, default: 0
-      - --clustalout Output: clustal format, default: fasta
-      - --retree number Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2
-      ]]>
-    </help>
-  <expand macro="citations" />
-</tool>
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Multiple alignment program for amino acid or nucleotide sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements" />
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <version_command><![CDATA[mafft --version]]></version_command>
+    <command><![CDATA[
+  ## Concatenate all input datasets no matter how they were provided
+  bash inputs.sh &&
+
+  ## Count total number of sequences across input datasets
+  ## Can't do this on the concatenated input data prepared above because it's
+  ## just a regular file and we don't have Galaxy-generated metadata for it.
+  #set sequence_count = 0
+  #if $input.mapping == "implicit"
+    #for $batch in $input.batches:
+      #set sequence_count += int($batch.inputs.metadata.sequences)
+    #end for
+  #elif $input.mapping == "merge"
+    #for $batch in $input.batches:
+      #for $dataset in $batch.inputs:
+        #set sequence_count += int($dataset.metadata.sequences)
+      #end for
+    #end for
+  #end if
+
+  ## For those cases in which MAFFT needs fasta3, set an env variable to make it
+  ## find the executable. Necessary because the current version of MAFFT still
+  ## expects a fasta34 executable in path, but we bundle a newer version.
+  #if $flavour.type == "custom"
+    #if $flavour.guidetree.guidetree_generation == "original"
+      #if $flavour.guidetree.dist_flavour.distance_method == "--fastapair"
+        export FASTA_4_MAFFT=`which @FASTA3_EXEC@` &&
+      #end if
+    #elif $flavour.guidetree.guidetree_generation == "parttree"
+      #if $flavour.guidetree.parttree_selection.parttree_option == "--fastaparttree"
+        export FASTA_4_MAFFT=`which @FASTA3_EXEC@` &&
+      #end if
+    #end if
+  #end if
+
+  ## groupsize warning
+  #if $flavour.type == "custom"
+    #if $flavour.guidetree.guidetree_generation == "parttree"
+      #if $flavour.guidetree.parttree_selection.groupsize > $sequence_count
+        echo "WARNING = Chosen groupsize number larger than number of input sequences. Not recommended for MAFFT." &&
+      #end if
+    #end if
+  #end if
+
+  ## run MAFFT with predefined MSA flavours or custom settings
+  #if $flavour.type == "custom"
+    mafft
+    #if $flavour.guidetree.guidetree_generation == "original"
+      #if $flavour.guidetree.dist_flavour.distance_method == "--6merpair"
+        --6merpair
+        --retree $flavour.guidetree.dist_flavour.retree
+      #elif $flavour.guidetree.dist_flavour.distance_method == "--globalpair"
+        --globalpair
+        --weighti $flavour.guidetree.dist_flavour.weighti
+        #if $flavour.guidetree.dist_flavour.treat_unrelated_segments.unalignlevel > 0
+          --allowshift --unalignlevel $flavour.guidetree.dist_flavour.treat_unrelated_segments.unalignlevel
+        #end if
+        $flavour.guidetree.dist_flavour.treat_unrelated_segments.leavegappyregion
+      #elif $flavour.guidetree.dist_flavour.distance_method == "--localpair"
+        --localpair
+        --weighti $flavour.guidetree.dist_flavour.weighti
+        --lop $flavour.guidetree.dist_flavour.lop
+        --lep $flavour.guidetree.dist_flavour.lep
+        --lexp $flavour.guidetree.dist_flavour.lexp
+      #elif flavour.guidetree.dist_flavour.distance_method == "--genafpair"
+        --genafpair
+        --weighti $flavour.guidetree.dist_flavour.weighti
+        --lop $flavour.guidetree.dist_flavour.lop
+        --lep $flavour.guidetree.dist_flavour.lep
+        --lexp $flavour.guidetree.dist_flavour.lexp
+        --LOP $flavour.guidetree.dist_flavour.LOP
+        --LEXP $flavour.guidetree.dist_flavour.LEXP
+      #elif $flavour.guidetree.dist_flavour.distance_method == "--fastapair"
+        --fastapair
+        --weighti $flavour.guidetree.dist_flavour.weighti
+      #end if
+    #elif $flavour.guidetree.guidetree_generation == "parttree"
+      $flavour.guidetree.parttree_selection.parttree_option
+      --retree $flavour.guidetree.parttree_selection.retree
+      --partsize $flavour.guidetree.parttree_selection.partsize
+      #if $flavour.guidetree.parttree_selection.groupsize != -1
+        --groupsize $flavour.guidetree.parttree_selection.groupsize
+      #end if
+    #end if
+    ## progressive alignment calculation
+    --maxiterate $flavour.progressive_alignment_calculation.maxiterate
+    $flavour.progressive_alignment_calculation.fft
+    $flavour.progressive_alignment_calculation.noscore
+  #else
+    $flavour.type
+    #if $flavour.type == "mafft-ginsi" or "--globalpair" in str($flavour.type)
+      #if $flavour.treat_unrelated_segments.unalignlevel > 0
+        --allowshift --unalignlevel $flavour.treat_unrelated_segments.unalignlevel
+      #end if
+      $flavour.treat_unrelated_segments.leavegappyregion
+    #end if
+  #end if
+
+  ## handle scoring matrix
+  $datatype_selection.datatype
+  #if $datatype_selection.datatype != ""
+    #if $datatype_selection.scoring_matrix.type == "custom"
+      --aamatrix '$datatype_selection.scoring_matrix.aamatrix'
+    #else
+      $datatype_selection.scoring_matrix.type $datatype_selection.scoring_matrix.coefficient
+    #end if
+    $datatype_selection.fmodel
+    ## gap penalties
+    #if $datatype_selection.gap_costs.use_defaults == "no"
+      --ep $datatype_selection.gap_costs.ep --op $datatype_selection.gap_costs.op
+    #end if
+  #end if
+
+
+  ## output options
+  $reorder
+  $outputFormat
+  $treeout
+
+  ## specify threads to use
+  ## disable multithreading during iterative refinement step for reproducibility
+  ## cmp. https://mafft.cbrc.jp/alignment/software/multithreading.html
+  --thread \${GALAXY_SLOTS:-1} --threadit 0
+
+  input.fa > '$outputAlignment'
+
+  ## Output alignment tree
+  #if $treeout
+    && mv input.fa.tree '$outputTree'
+  #end if
+    ]]></command>
+    <configfiles>
+        <configfile filename="inputs.sh"><![CDATA[
+  #if $input.mapping == "implicit"
+    #for $batch in $input.batches:
+cat $batch.inputs >> input.fa
+      #end for 
+  #elif $input.mapping == "merge"
+    #for $batch in $input.batches:
+      #for $dataset in $batch.inputs:
+cat $dataset >> input.fa
+      #end for
+    #end for
+  #end if
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="input">
+            <param name="mapping" type="select" label="For multiple inputs generate" help="All you have is a single dataset with the sequences to align? You can skip this help text and continue with the default setting. For multiple input datasets, the first mode will launch separate MAFFT jobs for all sequences from the first, second, ..., n-th dataset/element from each input batch, respectively, resulting in n separate MSAs. The second mode will concatenate all input sequences from all inputs for a single run of MAFFT and will generate a single MSA.">
+                <option value="implicit">one or several MSAs depending on input structure</option>
+                <option value="merge">a single MSA of all sequences from all inputs</option>
+            </param>
+            <when value="implicit">
+                <repeat name="batches" title="Input batch" default="1" min="1">
+                    <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format. Add Dataset for concatenation of every additional dataset with each file of the first upload panel"/>
+                </repeat>
+            </when>
+            <when value="merge">
+                <repeat name="batches" title="Input batch" default="1" min="1">
+                    <param name="inputs" multiple="true" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
+                </repeat>
+            </when>
+        </conditional>
+        <conditional name="datatype_selection">
+            <param name="datatype" type="select" label="Type of sequences" help="The tool can try to detect the type of the input sequences, but you likely want to declare it explicitly. Doing so will also give you control over the scoring matrix used for the alignment, while autodetection will result in the Kimura PAM200 and the BLOSUM62 matrix being used for nucleic acids and protein alignments, respectively.">
+                <option value="">auto-detect</option>
+                <option value="--nuc">Nucleic acids</option>
+                <option value="--amino">Amino acids</option>
+            </param>
+            <when value="" />
+            <when value="--nuc">
+                <conditional name="scoring_matrix">
+                    <param name="type" type="select" label="Type of scoring matrix" help="See the tool help below for details about the available options.">
+                        <option value="--kimura">Kimura</option>
+                    </param>
+                    <when value="--kimura">
+                        <param argument="--kimura" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" />
+                    </when>
+                </conditional>
+                <expand macro="misc_scoring_scheme" />
+            </when>
+            <when value="--amino">
+                <conditional name="scoring_matrix">
+                    <param name="type" type="select" label="Type of scoring matrix" help="See the tool help below for details about the available options.">
+                        <option value="--bl" selected="true">BLOSUM</option>
+                        <option value="--jtt">JTT</option>
+                        <option value="--tm">transmembrane protein-optimized JTT</option>
+                        <option value="custom">custom matrix</option>
+                    </param>
+                    <when value="--bl">
+                        <param argument="--bl" name="coefficient" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
+                            <option value="30">30</option>
+                            <option value="45">45</option>
+                            <option value="62" selected="true">62</option>
+                            <option value="80">80</option>
+                        </param>
+                    </when>
+                    <when value="--jtt">
+                        <param argument="--jtt" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" />
+                    </when>
+                    <when value="--tm">
+                        <param argument="--tm" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix"/>
+                    </when>
+                    <when value="custom">
+                        <param argument="--aamatrix" type="data" format="txt" label="User-defined AA scoring matrix" help="The expected format of the matrix is the same as that used by BLAST."/>
+                    </when>
+                </conditional>
+                <expand macro="misc_scoring_scheme" />
+            </when>
+        </conditional>
+        <conditional name="flavour">
+            <param name="type" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section. With 'Auto', the tool automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size from few to many respectively. Default setting: FFT-NS-2.">
+                <option value="mafft --auto">Auto</option>
+                <option value="mafft-fftns --retree 1">FFT-NS-1 (very fast, progressive method; use for &gt;2,000 sequences)</option>
+                <option value="mafft-fftns" selected="true">FFT-NS-2 (fast, progressive method)</option>
+                <option value="mafft-nwns">NW-NS-2 (fast, progressive method without FFT approximation)</option>
+                <option value="mafft --retree 1 --maxiterate 0 --nofft --parttree">NW-NS-PartTree-1 (very fast, progressive method using the PartTree algorithm; for ~10,000 to ~50,000 sequences)</option>
+                <option value="mafft --maxiterate 0 --globalpair">G-INS-1 (slow, progressive method with an accurate guide tree)</option>
+                <option value="mafft-fftnsi">FFT-NS-i (slow, iterative refinement method)</option>
+                <option value="mafft-nwnsi">NW-NS-i (slow, iterative refinement method without FFT approximation)</option>
+                <option value="mafft-einsi">E-INS-i (very slow; use for &lt;200 sequences with multiple conserved domains and long gaps)</option>
+                <option value="mafft-linsi">L-INS-i (very slow; use for &lt;200 sequences with one conserved domain and long gaps)</option>
+                <option value="mafft-ginsi">G-INS-i (very slow; recommended for &lt;200 sequences with global homology)</option>
+                <option value="custom">Custom Parameters</option>
+            </param>
+            <when value="mafft --auto"/>
+            <when value="mafft-fftns --retree 1"/>
+            <when value="mafft-fftns"/>
+            <when value="mafft-nwns"/>
+            <when value="mafft --retree 1 --maxiterate 0 --nofft --parttree"/>
+            <when value="mafft --maxiterate 0 --globalpair">
+                <expand macro="global_align_options"/>
+            </when>
+            <when value="mafft-fftnsi"/>
+            <when value="mafft-nwnsi"/>
+            <when value="mafft-einsi"/>
+            <when value="mafft-linsi"/>
+            <when value="mafft-ginsi">
+                <expand macro="global_align_options"/>
+            </when>
+            <when value="custom">
+                <conditional name="guidetree">
+                    <param name="guidetree_generation" type="select" label="GuideTree-Generation" help="Parttree is recommended for a large number (> ~10,000) of sequences as input">
+                        <option value="original">Original guidetree building method of MAFFT</option>
+                        <option value="parttree">Fast guidetree building method with PartTree-algorithm</option>
+                    </param>
+                    <when value="original">
+                        <conditional name="dist_flavour">
+                            <param name="distance_method" type="select" label="Distance method" help="Distance method must be chosen regarding your data">
+                                <option value="--6merpair" selected="true">Shared 6mers distance (fastest) (--6merpair)</option>
+                                <option value="--globalpair">Global alignment (Needleman-Wunsch) (--globalpair)</option>
+                                <option value="--localpair">Local alignment (Smith-Waterman) (--localpair)</option>
+                                <option value="--genafpair">Local, affine gap cost (--genafpair)</option>
+                                <option value="--fastapair">All pairwise alignments are computed with FASTA (--fastapair)</option>
+                            </param>
+                            <when value="--6merpair">
+                                <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is build this number of times in the progressive stage."/>
+                            </when>
+                            <when value="--globalpair">
+                                <expand macro="global_align_options"/>
+                                <expand macro="weighti_param" />
+                            </when>
+                            <when value="--localpair">
+                                <expand macro="weighti_param" />
+                                <param argument="--lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value"/>
+                                <param argument="--lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value"/>
+                                <param argument="--lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
+                            </when>
+                            <when value="--genafpair">
+                                <expand macro="weighti_param" />
+                                <param argument="--lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
+                                <param argument="--lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
+                                <param argument="--lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
+                                <param argument="--LOP" type="float" value="-6.00" label="Gap opening penalty to skip the alignment" help="-6.00 default value" />
+                                <param argument="--LEXP" type="float" value="0.00" label="Gap extension penalty to skip the alignment" help="0 default value" />
+                            </when>
+                            <when value="--fastapair">
+                                <expand macro="weighti_param" />
+                            </when>
+                        </conditional>
+                    </when>
+                    <when value="parttree">
+                        <conditional name="parttree_selection">
+                            <param name="parttree_option" type="select" label="Which distance for the fast tree-building method?">
+                                <option value="--parttree" selected="true">Fast tree-building method with the 6mer distance (--parttree)</option>
+                                <option value="--fastaparttree">Distances based on FASTA (--fastaparttree)</option>
+                                <option value="--dpparttree">Distances based on DP. (Needleman-Wunsch) (--dpparttree)</option>
+                            </param>
+                            <when value="--parttree">
+                                <expand macro="parttree_parameters" />
+                            </when>
+                            <when value="--fastaparttree">
+                                <expand macro="parttree_parameters" />
+                            </when>
+                            <when value="--dpparttree">
+                                <expand macro="parttree_parameters" />
+                            </when>
+                        </conditional>
+                    </when>
+                </conditional>
+                <section name="progressive_alignment_calculation" title="Progressive alignment calculation" expanded="true">
+                    <param argument="--maxiterate" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
+                    <param argument="--fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
+                    <param argument="--noscore" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
+                </section>
+            </when>
+        </conditional>
+        <param argument="--reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" help="Default order is input order." />
+        <param argument="--treeout" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Keep alignment tree as output?" />
+        <param name="outputFormat" type="select" label="Output format">
+            <option value="" selected="true">FASTA</option>
+            <option value="--clustalout">ClustalW</option>
+            <option value="--phylipout">Phylip</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
+            <change_format>
+                <when input="outputFormat" value="--clustalout" format="clustal"/>
+                <when input="outputFormat" value="--phylipout" format="phylip"/>
+            </change_format>
+        </data>
+        <data name="outputTree" format="txt" label="${tool.name} Guide Tree">
+            <filter>treeout</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_amino.fa"/>
+                </repeat>
+            </conditional>
+            <output name="outputAlignment" ftype="fasta" file="mafft_default.aln"/>
+        </test>
+        <!-- test autodetection of suitable algorithm from input; expected to choose L-INS-i -->
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_amino.fa"/>
+                </repeat>
+            </conditional>
+             <conditional name="flavour">
+                <param name="type" value="mafft --auto"/>
+            </conditional>
+            <output name="outputAlignment" ftype="fasta" file="mafft_auto_linsi.aln"/>
+        </test>
+        <!-- test explicit specification of L-INS-i mode -->
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_amino.fa"/>
+                </repeat>
+            </conditional>
+             <conditional name="flavour">
+                <param name="type" value="mafft-linsi"/>
+            </conditional>
+            <output name="outputAlignment" ftype="fasta" file="mafft_auto_linsi.aln"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_amino.fa"/>
+                </repeat>
+            </conditional>
+            <conditional name="datatype_selection">
+                <param name="datatype" value="--amino"/>
+                <conditional name="scoring_matrix">
+                    <param name="type" value="--bl"/>
+                    <param name="coefficient" value="80"/>
+                </conditional>
+            </conditional>
+            <conditional name="flavour">
+                <param name="type" value="mafft-fftns"/>
+            </conditional>
+            <param name="outputFormat" value="--clustalout"/>
+            <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" />
+        </test>
+        <test expect_num_outputs="1" >
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_nuc.fa"/>
+                </repeat>
+            </conditional>
+            <conditional name="datatype_selection">
+                <param name="datatype" value="--nuc"/>
+                <conditional name="scoring_matrix">
+                    <param name="type" value="--kimura"/>
+                    <param name="coefficient" value="40"/>
+                </conditional>
+            </conditional>
+            <conditional name="flavour">
+                <param name="type" value="mafft-fftns"/>
+            </conditional>
+            <param name="outputFormat" value="--phylipout"/>
+            <output name="outputAlignment" ftype="phylip" file="mafft_kimura40.phylip.aln" />
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_amino.fa"/>
+                </repeat>
+            </conditional>
+            <conditional name="datatype_selection">
+                <param name="datatype" value="--amino"/>
+            </conditional>
+            <conditional name="flavour">
+                <param name="type" value="custom"/>
+                <conditional name="guidetree">
+                    <param name="guidetree_generation" value="original"/>
+                    <conditional name="dist_flavour">
+                        <param name="distance_method" value="--globalpair"/>
+                        <param name="weighti" value="3"/>
+                    </conditional>
+                </conditional>
+                <section name="progressive_alignment_calculation">
+                    <param name="maxiterate" value="1000"/>
+                </section>
+            </conditional>
+            <param name="outputFormat" value="--clustalout"/>
+            <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln">
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="input">
+                <param name="mapping" value="implicit"/>
+                    <repeat name="batches">
+                        <param name="inputs" value="sample_amino.fa"/>
+                    </repeat>
+            </conditional>
+            <conditional name="datatype_selection">
+                <param name="datatype" value="--amino"/>
+            </conditional>
+            <conditional name="flavour">
+                <param name="type" value="custom"/>
+                <conditional name="guidetree">
+                    <param name="guidetree_generation" value="parttree"/>
+                    <conditional name="parttree_selection">
+                        <param name="parttree_option" value="--parttree"/>
+                        <param name="retree" value="2"/>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <output name="outputAlignment" ftype="fasta" file="mafft_custom_parttree.aln" />
+        </test>
+        <!-- test concatenation of multiple inputs -->
+        <test expect_num_outputs="2">
+            <conditional name="input">
+                <param name="mapping" value="merge"/>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_amino.fa"/>
+                </repeat>
+                <repeat name="batches">
+                    <param name="inputs" value="sample_nuc.fa"/>
+                </repeat>
+            </conditional>
+            <param name="treeout" value="true"/>
+            <output name="outputAlignment" ftype="fasta">
+                <metadata name="sequences" value="39"/>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+MAFFT is a multiple sequence alignment (MSA) program, which offers a range of multiple alignment methods.
+
+Input types and alignment scoring matrices
+------------------------------------------
+
+For the alignment of *protein* sequences, you can choose between:
+
+- different flavors of BLOSUM matrices (`Henikoff S and Henikoff JG, 1992 <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC50453/>`__)
+- JTT matrices with any point accepted mutation (PAM) rate (`Jones, Taylor and Thornton, 1992 <https://pubmed.ncbi.nlm.nih.gov/1633570/>`__)
+- PAM-based matrices optimized for transmembrane proteins (`Jones, Taylor and Thornton, 1994 <https://pubmed.ncbi.nlm.nih.gov/8112466/>`__)
+
+For nucleic acid sequence alignment, MAFFT uses Kimura's two parameter model (`Kimura 1980 <https://pubmed.ncbi.nlm.nih.gov/7463489/>`__)
+with a transitions to transversions ratio of 2 (kappa 2), but lets you configure the PAM value.
+
+The tool can also try to autodetect the sequence type from the input(s).
+In this mode, it will use the BLOSUM 62 matrix if it detects amino acids input, and the Kimura kappa 2 PAM200 matrix for nucleic acids.
+
+
+Pre-configured MSA methods
+--------------------------
+
+From the `MAFFT man page <https://mafft.cbrc.jp/alignment/software/manual/manual.html>`__, an overview of the different predefined flavours of the tool.
+
+**Accuracy-oriented methods:**
+
+- *L-INS-i* (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
+
+      - mafft --localpair --maxiterate 1000 input [> output]
+- *G-INS-i* (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
+
+      - mafft --globalpair --maxiterate 1000 input [> output]
+- *E-INS-i* (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
+
+      - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
+
+**Speed-oriented methods:**
+
+- *FFT-NS-i* (iterative refinement method; two cycles only):
+
+    - mafft --retree 2 --maxiterate 2 input [> output]
+- *FFT-NS-2* (fast; progressive method):
+
+    - mafft --retree 2 --maxiterate 0 input [> output]
+- *NW-NS-i* (iterative refinement method without FFT approximation; two cycles only):
+
+    - mafft --retree 2 --maxiterate 2 --nofft input [> output]
+- *NW-NS-2* (fast; progressive method without the FFT approximation):
+
+    - mafft --retree 2 --maxiterate 0 --nofft input [> output]
+- *NW-NS-PartTree-1* (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
+
+    - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
+- *FFT-NS-1* (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
+
+    - mafft --retree 1 --maxiterate 0 input [> output]
+    ]]></help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_auto_linsi.aln	Wed Mar 20 07:34:52 2024 +0000
@@ -0,0 +1,504 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+M------------------NGTE-G------DNFYVPF----SNKTGLARSPYEYPQY--
+--------------------------------------------------YLAEPW----
+---------------KYSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLA
+MANLFMVLFG-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERY
+IVICKPMGNF-RFGNTHAIMGVAFTWIMALAC-AAPPLVG-WS-----RYIPEGMQCSCG
+PDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQESA-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEKEVTRMVVLMVIGFLVCWVPYAS
+VAFYIFT---HQGS-DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTL-----
+CC-----GKNPLGDDE-SGA-STSK-TEVSSVS-TSPVSPA-------------------
+------------------------------------------------------------
+---------------
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+M------------------NGTE-G------PNFYVPF----SNITGVVRSPFEQPQY--
+--------------------------------------------------YLAEPW----
+---------------QFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA
+VADLFMVFGG-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERY
+VVVCKPMSNF-RFGENHAIMGVAFTWVMALAC-AAPPLVG-WS-----RYIPEGMQCSCG
+IDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESA-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------TTQKAEKEVTRMVIIMVIFFLICWLPYAS
+VAMYIFT---HQGS-NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSL-----
+CC-----GKNPLGDDE-ASA-TASK-TETSQVA-PA------------------------
+------------------------------------------------------------
+---------------
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+M------------------NGTE-G------INFYVPM----SNKTGVVRSPFEYPQY--
+--------------------------------------------------YLAEPW----
+---------------KYRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLA
+VADLFMACFG-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERY
+IVVCKPMGNF-RFSATHAMMGIAFTWVMAFSC-AAPPLFG-WS-----RYMPEGMQCSCG
+PDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQESA-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------TTQKAEKEVTRMVILMVLGFMLAWTPYAV
+VAFWIFT---NKGA-DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTI-----
+CC-----GKNPFGDEDVSSTVSQSK-TEVSSVS-SSQVSPA-------------------
+------------------------------------------------------------
+---------------
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+M------------------NGTE-G------KNFYVPM----SNRTGLVRSPFEYPQY--
+--------------------------------------------------YLAEPW----
+---------------QFKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLA
+VAGTIMVCFG-FTVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERY
+IVVCKPMGSF-KFSSSHAFAGIAFTWVMALAC-AAPPLFG-WS-----RYIPEGMQCSCG
+PDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDSA-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEREVTKMVILMVFGFLIAWTPYAT
+VAAWIFF---NKGA-DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTI-----
+FC-----GKNPLGDDE-SSTVSTSK-TEVSSVS-PA------------------------
+------------------------------------------------------------
+---------------
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+M------------------NGTE-G------NNFYVPL----SNRTGLVRSPFEYPQY--
+--------------------------------------------------YLAEPW----
+---------------QFKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLA
+VAGAIMVCFG-FTVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERY
+IVVCKPMGSF-KFSSTHASAGIAFTWVMAMAC-AAPPLVG-WS-----RYIPEGIQCSCG
+PDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDSA-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEREVTKMVILMVLGFLVAWTPYAT
+VAAWIFF---NKGA-AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTL-----
+FC-----GKNPLGDEE-SSTVSTSK-TEVSSVS-PA------------------------
+------------------------------------------------------------
+---------------
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+M------------------KQVP-EFH----EDFYIPIPL--DINNLSAYSPFLVPQD--
+--------------------------------------------------HLGNQG----
+---------------IFMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLS
+IANLFVAIFG-SPLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERW
+LVICKPLGNF-TFKTPHAIAGCILPWISALAA-SLPPLFG-WS-----RYIPEGLQCSCG
+PDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKAQADSA-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEREVTKMVVVMVLGFLVCWAPYAS
+FSLWIVS---HRGE-EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMMKMV-----
+C------GKN-IEEDE-AST-SSQV-TQVSSVA-PEK-----------------------
+------------------------------------------------------------
+---------------
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+M------------------RKMS-E------EEFYL-------FKNISSVGPWDGPQY--
+--------------------------------------------------HIAPVW----
+---------------AFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVS
+FGGFLLCIFS-VFPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERY
+IVICKPFGNF-RFSSKHALTVVLATWTIGIGV-SIPPFFG-WS-----RFIPEGLQCSCG
+PDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESA-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------TTQKAEREVSRMVVVMVGSFCVCYVPYAA
+FAMYMVN---NRNH-GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIMKMV-----
+C------GKA-MTDES-DTC-SSQK-TEVSTVS-STQVGPN-------------------
+------------------------------------------------------------
+---------------
+>     8=opsin, greensensitive  human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--DLAETVIA-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERW
+LVVCKPFGNV-RFDAKLAIVGIAFSWIWAAVW-TAPPIFG-WS-----RYWPHGLKTSCG
+PDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESE-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEKEVTRMVVVMVLAFC--------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDSYEDSTQS------SIFTY-------TNSNSTRGPFEGPNY--
+--------------------------------------------------HIAPRW----
+---------------VYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLA
+VADLAETVIA-STISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERW
+MVVCKPFGNV-RFDAKLAIVGIAFSWIWAAVW-TAPPIFG-WS-----RYWPHGLKTSCG
+PDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESE-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEKEVTRMVVVMVLAFCFCWGPYAF
+FACFAAA---NPGY-PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLF-----
+-------GKK-VDDGS-ELS-SASK-TEVSSVS---SVSPA-------------------
+------------------------------------------------------------
+---------------
+>    10== Z68193   1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDSYEDSTQS------SIFTY-------TNSNSTRGPFEGPNY--
+--------------------------------------------------HIAPRW----
+---------------VYHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLA
+VADLAETVIA-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERW
+LVVCKPFGNV-RFDAKLAIVGIAFSWIWSAVW-TAPPIFG-WS-----RYWPHGLKTSCG
+PDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYLQVWLAIRAVAKQQKESE-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEKEVTRMVVVMIFAYCVCWGPYTF
+FACFAAA---NPGY-AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLF-----
+-------GKK-VDDGS-ELS-SASK-TEVSSVS---SVSPA-------------------
+------------------------------------------------------------
+---------------
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDD-DDTTRG------SVFTY-------TNTNNTRGPFEGPNY--
+--------------------------------------------------HIAPRW----
+---------------VYNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLA
+FVDLVETLVA-STISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERW
+FVVCKPFGNI-KFDSKLAIIGIVFSWVWAWGW-SAPPIFG-WS-----RYWPHGLKTSCG
+PDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQVWMAIRAVAAQQKESE-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEREVSRMVVVMIVAFCICWGPYAS
+FVSFAAA---NPGY-AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLF-----
+-------GKK-VDDGS-EAS-TTSR-TEVSSVS-NSSVAPA-------------------
+------------------------------------------------------------
+---------------
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MA-AWE-AAFAARRRHEE-EDTTRD------SVFTY-------TNSNNTRGPFEGPNY--
+--------------------------------------------------HIAPRW----
+---------------VYNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLA
+VADLGETVIA-STISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERW
+FVVCKPFGNI-KFDGKLAVAGILFSWLWSCAW-TAPPIFG-WS-----RYWPHGLKTSCG
+PDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVWLAIRAVAAQQKESE-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------STQKAEKEVSRMVVVMIVAYCFCWGPYTF
+FACFAAA---NPGY-AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCILQLF-----
+-------GKK-VDDGS-EVS-T-SR-TEVSSVS-NSSVSPA-------------------
+------------------------------------------------------------
+---------------
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+-----------------------MS------SNSSQ-------APPNGTPGPFDGPQW--
+-------------------------------------------------PYQAPQS----
+---------------TYVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLA
+VADLLVTLCG-SSVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERY
+VVVCKPLGDF-QFQRRHAVSGCAFTWGWALLW-SAPPLLG-WS-----SYVPEGLRTSCG
+PNWYTGGSN--NNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEAD-------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------TTQRAEREVTRMVIVMVMAFLLCWLPYST
+FALVVAT---HKGI-IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLLEML-----
+CCGYQ--PQR-TGKAS-PGT-PGPH-ADVTAAGLRNKVMPAHPV----------------
+------------------------------------------------------------
+---------------
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+M------------------ESGNVS------SSLF------------GNVSTALRPEA--
+-------------------------RLSA---E---TRLLGWNVPPEELRHIPEHWLTYP
+----------EPPESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLA
+FCDFMMMVK--TPIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRF
+NVITRPMEG--KMTHGKAIAMIIFIYMYATPW-VVACYTETWG-----RFVPEGYLTSCT
+FDYLTDN--FDTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKMNVES
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS-------NVDKNKETAEIRIAKAAITICFLFFCSWTPYGV
+MSLIGAF---GDKT-LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWL--
+AL-----NEK-APESS-AVA-STST-TQEPQQT---------------------------
+TAA---------------------------------------------------------
+---------------
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+M------------------EYHNVS------SVL-------------GNVSSVLRPDA--
+-------------------------RLSA---E---SRLLGWNVPPDELRHIPEHWLIYP
+----------EPPESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLA
+FCDFMMMIK--TPIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRY
+NVITRPMEG--KMTHGKAIAMIIFIYLYATPW-VVACYTESWG-----RFVPEGYLTSCT
+FDYLTDN--FDTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKMNVDS
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS-------NVDKSKEAAEIRIAKAAITICFLFFASWTPYGV
+MSLIGAF---GDKT-LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWL--
+AI-----SEK-APESR-AAI-STST-TQEQQQT---------------------------
+TAA---------------------------------------------------------
+---------------
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+M------------------EPLC------------------------NASEPPLRPEA--
+-------------------------R-SSGNGD---LQFLGWNVPPDQIQYIPEHWLTQL
+----------EPPASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLA
+VFDLIMCLK--APIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRY
+NVITKPMNR--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFWD-----RFVPEGYLTSCS
+FDYLSDN--FDTRLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKKMNVES
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS-------NVDKSKETAEIRIAKAAITICFLFFVSWTPYGV
+MSLIGAF---GDKS-LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWL--
+GV-----NEK-SGEIS-SAQ-STTT-QEQQQTT---------------------------
+AA----------------------------------------------------------
+---------------
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+M------------------DALC------------------------NASEPPLRPEA--
+-------------------------RMSSGSDE---LQFLGWNVPPDQIQYIPEHWLTQL
+----------EPPASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLA
+VFDLIMCLK--APIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRY
+NVITKPMNR--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFWD-----RFVPEGYLTSCS
+FDYLSDN--FDTRLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKKMNVES
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS-------NVDKSKETAEIRIAKAAITICFLFFVSWTPYGV
+MSLIGAF---GDKS-LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWL--
+GV-----NEK-SGEAS-SAQ-STTT-QEQTQQT---------------------------
+SAA---------------------------------------------------------
+---------------
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+M------------------TNAT-------------------------------GPQMAY
+-------YG--------------AASMDFGYPE---GVSIVDFVRPEIKPYVHQHWYNYP
+----------PVNPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLA
+LSDLIMLTTN-VPFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRY
+NIICNGFNGP-KLTTGKAVVFALISWVIAIGC-ALPPFFG-WG-----NYILEGILDSCS
+YDYLTQD--FNTFSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKKMNVST
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS--------NEADAQRAEIRIAKTALVNVSLWFICWTPYAL
+ISLKGVM---GDTS-GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWF--
+CV-----HET-ETKSN-DDS-QSNS-TVAQDKA---------------------------
+------------------------------------------------------------
+---------------
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+M------------------ANVT-------------------------------GPQMAF
+-------YG--------------SGAATFGYPE---GMTVADFVPDRVKHMVLDHWYNYP
+----------PVNPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLA
+LSDLIMLTTN-FPPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRY
+NIICNGFNGP-KLTQGKATFMCGLAWVISVGW-SLPPFFG-WG-----SYTLEGILDSCS
+YDYFTRD--MNTITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKKMNVTN
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS--------NEAETQRAEIRIAKTALVNVSLWFICWTPYAA
+ITIQGLL---GNAE-GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWF--
+CV-----HEK-DPNDV-EEN-QSSN-TQTQEKS---------------------------
+------------------------------------------------------------
+---------------
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+M------------------ESFA-------------------------VAAAQLGPHF--
+------------------------APLS--------NGSVVDKVTPDMAHLISPYWNQFP
+----------AMDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLA
+ISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRY
+QVIVKGMAGR-PMTIPLALGKM---------------------------YVPEGNLTSCG
+IDYLERD--WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKS
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS--------SEDAEKSAEGKLAKVALVTITLWFMAWTPYLV
+INCMGLF---KF-E-GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCC--
+VF-----GKV-DDGKS-SDA-QSQA-TASEAES------KA-------------------
+------------------------------------------------------------
+---------------
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+M------------------ESFA-------------------------VAAAQLGPHF--
+------------------------APLS--------NGSVVDKVTPDMAHLISPYWNQFP
+----------AMDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLA
+ISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRY
+QVIVKGMAGR-PMTIPLALGKIAYIWFMSSIW-CLAPAFG-WS-----RYVPEGNLTSCG
+IDYLERD--WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKS
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS--------SEDAEKSAEGKLAKVALVTITLWFMAWTPYLV
+INCMGLF---KF-E-GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCC--
+VF-----GKV-DDGKS-SDA-QSQA-TASEAES------KA-------------------
+------------------------------------------------------------
+---------------
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+M------------------DSFA-------------------------AVATQLGPQF--
+------------------------AAPS--------NGSVVDKVTPDMAHLISPYWDQFP
+----------AMDPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLA
+ISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRY
+QVIVKGMAGR-PMTIPLALGKIAYIWFMSTIWCCLAPVFG-WS-----RYVPEGNLTSCG
+IDYLERD--WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKS
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS--------SEDADKSAEGKLAKVALVTISLWFMAWTPYLV
+INCMGLF---KF-E-GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCC--
+VF-----GKV-DDGKS-SEA-QSQA-TTSEAES------KA-------------------
+------------------------------------------------------------
+---------------
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+M------------------ERSH--------------------LPETPFDLAHSGPRF--
+------------------------QAQSSG------NGSVLDNVLPDMAHLVNPYWSRFA
+----------PMDPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLA
+FSDFCMMASQ-SPVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRY
+NVIVKGINGT-PMTIKTSIMKILFIWMMAVFW-TVMPLIG-WS-----AYVPEGNLTACS
+IDYMTRM--WNPRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKKMNVKS
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS--------SEDCDKSAEGKLAKVALTTISLWFMAWTPYLV
+ICYFGLF---KI-D-GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMC--
+VF-----GNT-DEPKP-DAP-ASDTETTSEADS------KA-------------------
+------------------------------------------------------------
+---------------
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+M------------------ERSL--------------------LPEPPLAMALLGPRF--
+------------------------EAQTGG------NRSVLDNVLPDMAPLVNPHWSRFA
+----------PMDPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLA
+FSDFCMMASQ-SPVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRY
+NVIVKGINGT-PMTIKTSIMKIAFIWMMAVFW-TIMPLIG-WS-----SYVPEGNLTACS
+IDYMTRQ--WNPRSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKKMNVKS
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS--------SEDCDKSAENKLAKVALTTISLWFMAWTPYLI
+ICYFGLF---KI-D-GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMC--
+VC-----GTT-DEPKP-DAP-PSDTETTSEAES------KD-------------------
+------------------------------------------------------------
+---------------
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+M-------------------------------------------------IAVSGPSY--
+------------------------EAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYP
+----------PLNPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLA
+ISNFLMMFCM-SPPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRY
+NVIVKGLSGK-PLSINGALIRIIAIWLFSLGW-TIAPMFG-WN-----RYVPEGNMTACG
+TDYFNRG--LLSASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKKMNVAS
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRS--------SENQNTSAECKLAKVALMTISLWFMAWTPYLV
+INFSGIF---NL-V-KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSL--
+AC-----AA--EPSSD-AVS-TTSG-TTTVTDN------EK------------------S
+NA----------------------------------------------------------
+---------------
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+M------------------ANQL---------------------------------SY--
+------------------------SSLGWPYQP---NASVVDTMPKEMLYMIHEHWYAFP
+----------PMNPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLA
+FSDFCMMAFM-MPTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRY
+NVIVRGMAAA-PLTHKKATLLLLFVWIWSGGW-TILPFFG-WS-----RYVPEGNLTSCT
+VDYLTKD--WSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKKMNVAS
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRA-------NADQQKQSAECRLAKVAMMTVGLWFMAWTPYLI
+ISWAGVF---SSGT-RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSL--
+AC-----GSG-ESGSD-VKS-EASA-TTTMEEK------PKIPEA---------------
+------------------------------------------------------------
+---------------
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+M------------------VEST----------------------TLVNQTWWYNPTV--
+--------------------------------------------------DIHPHWAKFD
+----------PIPDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLA
+MSDLSFSAINGFPLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRY
+NVIGRPMAASKKMSHRRAFLMIIFVWMWSIVW-SVGPVFN-WG-----AYVPEGILTSCS
+FDYLSTD--PSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKRLNAKE
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRK---------AQAGASAEMKLAKISMVIITQFMLSWSPYAI
+IALLAQF---GPAE-WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLT
+CCQFD------EKECE-DAN-DAEE-EVVASER----GGESRDAAQMKEMMAMMQKMQAQ
+QAAYQP---PPPPQGYPPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAP
+QGAPPQGVDNQAYQA
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+M------------------GRDL-----------------------RDNETWWYNPSI--
+--------------------------------------------------VVHPHWREFD
+----------QVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLA
+FSDFTFSLVNGFPLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRY
+NVIGRPMAASKKMSHRRAFIMIIFVWLWSVLW-AIGPIFG-WG-----AYTLEGVLCNCS
+FDYISRD--STTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKE
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LRK---------AQAGANAEMRLAKISIVIVSQFLLSWSPYAV
+VALLAQF---GPLE-WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLT
+CCQFD------DKETE-DDK-DAET-EIPAGES--SDAAPSADAAQMKEMMAMMQKMQQQ
+QAAYPPQGYAPPPQGYPPQGYPPQGY--PPQGYPPQGYPP---PPQGAPPQGAPP-----
+-AAPPQGVDNQAYQA
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MM-----------------DVNSSGR-----PDLYGHLRS-FLLPEVGRGLPDLSPDG--
+----------GADPVAGSWAP---HLLS------------------EVTASPAPTWDAPP
+DNASGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLA
+LADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRY
+LGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKVCLIS
+QDF----------GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPG-------
+-------FPRVEPDSVIALNG---------------------------------------
+-----------------------IVKLQKE-------------------VEECAN-----
+-------------LSRLLKHE------RKNISIFKREQKAATTLGIIVGAFTVCWLPFFL
+LSTARPFICGTSCS-CIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLL-----
+QCQYRNINRK-------LSAAGMHE-ALKLAER------PERPEFVL------------Q
+NADY--------------------------------------------------------
+-------CRKKGHDS
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+M-----------------------------------------------------------
+--------------------P---HLLS--------GFL-------EVTASPAPTWDAPP
+DNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLA
+LADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRY
+LGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKVCLIS
+QDF----------GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPG-------
+-------FPRVQPESVISLNG---------------------------------------
+-----------------------VVKLQKE-------------------VEECAN-----
+-------------LSRLLKHE------RKNISIFKREQKAATTLGIIVGAFTVCWLPFFL
+LSTARPFICGTSCS-CIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLL-----
+QCQYRNINRK-------LSAAGMHE-ALKLAER------PERSEFVL------------Q
+NSDH--------------------------------------------------------
+-------CGKKGHDT
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+M-----------------------------------------------------------
+--------------------P---HLLS--------GFL-------EVTASPAPTWDAPP
+DNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLA
+LADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRY
+LGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKVCLIS
+QDF----------GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPG-------
+-------FPRVQPESVISLNG---------------------------------------
+-----------------------VVKLQKE-------------------VEECAN-----
+-------------LSRLLKHE------RKNISIFKREQKAATTLGIIVGAFTVCWLPFFL
+LSTARPFICGTSCS-CIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLL-----
+QCQYRNINRK-------LSAAGMHE-ALKLAER------PERSEFVL------------Q
+NSDH--------------------------------------------------------
+-------CGKKGHDT
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+M------------------DVLSPG-------------------------------QG--
+------------------------NNTTSPPAPF-E---------------TGGNTTGIS
+----------DVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLA
+VTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRY
+WAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDACTIS
+KDH----------GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT
+RHGASPAPQPKK-----SVNGE--SGSRNWRLGVESKAGGALC-----------------
+-------------------------------ANGAVRQGDDGAALEVIEVHRVGNSKEHL
+PLPSEAG--PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFI
+VALVLPF---CESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKII-----
+KCKFCRQ-----------------------------------------------------
+------------------------------------------------------------
+---------------
+>    33=p A35181 serotonin receptor class 1A - rat
+M------------------DVFSFG-------------------------------QG--
+------------------------NNTTASQEPF-G---------------TGGNVTSIS
+----------DVTFSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLA
+VTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRY
+WAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDACTIS
+KDH----------GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT
+SLGTSSAPPPKK-----SLNGQ--PGSGDWRRCAENRAVGTPC-----------------
+-------------------------------TNGAVRQGDDEATLEVIEVHRVGNSKEHL
+PLPSESG--SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFI
+VALVLPF---CESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKII-----
+KCKFCRR-----------------------------------------------------
+------------------------------------------------------------
+---------------
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+M------------------ANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLV
+TSDFNDSYGLTGQFINGSHSSRSRDNASANDT--------------SATNMTDDRYWSLT
+----------VYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLA
+VADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRY
+WAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIIS
+QDK----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKT
+EETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPEN
+ANGVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAML-ERQCNNGKK--
+-----------------ISSNDTPYSRTREKLELKRERKAARTLAIITGAFLICWLPFFI
+IALIGPF---VDPE-GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----
+FGKYRRGHR---------------------------------------------------
+------------------------------------------------------------
+---------------
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+M------------------ANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLV
+TSDFNDSYGLTGQFINGSHSSRSRDNASANDT--------------SATNMTDDRYWSLT
+----------VYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLA
+VADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRY
+WAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIIS
+QDK----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKT
+EETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPEN
+ANGVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAML-ERQCNNGKK--
+-----------------ISSNDTPYSRTREKLELKRERKAARTLAIITGAFLICWLPFFI
+IALIGPF---VDPE-GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----
+FGKYRRGHR---------------------------------------------------
+------------------------------------------------------------
+---------------
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+M------------------EGAE-GQEELDWEALYLRLPL--------------------
+------------------------QNCSWNSTGWEPNW--------NVTVVPNTTWWQAS
+-----APFDTPAALVRAAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLA
+VADLLVACLV-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRY
+WAVTN-IDYIHASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVS
+QDV----------GYQIFATASSFYVPVLIILILYWRIYQTARKRIRRRRGATARGGVGP
+-------PP-----------------------------------------------VPAG
+GALVAGGGSGGIAAAVVAVIGRPLPTISETTTTGFTNVSSNNTSPE---KQSCANGLEAD
+PPTTGYGAVAAAYYPSLVRRK------PKEAADSKRERKAAKTLAIITGAFVACWLPFFV
+LAILVPT---CDCE--VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLL-----
+CGRRVRRRRA-----------------------------PQ-------------------
+------------------------------------------------------------
+---------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_custom_original.clustal.aln	Wed Mar 20 07:34:52 2024 +0000
@@ -0,0 +1,496 @@
+CLUSTAL format alignment by MAFFT G-INS-i (v7.520)
+
+
+1==             MN----------------------------------------------------------
+2==             MN----------------------------------------------------------
+3==             MN----------------------------------------------------------
+4=p             MN----------------------------------------------------------
+5=p             MN----------------------------------------------------------
+6==             MK----------------------------------------------------------
+7==             MR----------------------------------------------------------
+8=opsin,        ------------------------------------------------------------
+9==             MA------QQWS-LQRLAGRHPQDS--------------------------YED------
+10==            MA------QQWS-LQRLAGRHPQDS--------------------------YED------
+11==            MT------EAWNVAVFAARRSRDD----------------------------DD------
+12==            MA-------AWE-AAFAARRRHEE----------------------------ED------
+13==            MS----------------------------------------------------------
+14==            MESGNVS-----------------------------------------------------
+15==            MEYHNVS-----------------------------------------------------
+16==            ME----------------------------------------------------------
+17==            MD----------------------------------------------------------
+18==            MT----------------------------------------------------------
+19==            MA----------------------------------------------------------
+20==            MESF--------------------------------------------------------
+21==            MESF--------------------------------------------------------
+22==            MDSF--------------------------------------------------------
+23==            MERSHLP---------------------------------------------------ET
+24==            MERSLLP---------------------------------------------------EP
+25==            MI----------------------------------------------------------
+26==            M-----------------------------------------------------------
+27==            MV----------------------------------------------------------
+28==            MG----------------------------------------------------------
+29==            MMDVN-----------SSGRPDLYGHLRSFLLPEVGRGLPDLSPDG------------GA
+30==            M-----------------------------------------------------------
+31=p            M-----------------------------------------------------------
+32==            MDVLS-------------------------------------------------------
+33=p            MDVFS-------------------------------------------------------
+34==            MANFTFGDLALD-VARMGGLASTPSGLRS-----TGLTTPGLSPTGLVTSDFNDSYGLTG
+35=p            MANFTFGDLALD-VARMGGLASTPSGLRS-----TGLTTPGLSPTGLVTSDFNDSYGLTG
+36==            ME----------------------------------------------------------
+                                                                            
+
+1==             ----GTEG--DNFY------------VPFSNKTG----------------------LARS
+2==             ----GTEG--PNFY------------VPFSNITG----------------------VVRS
+3==             ----GTEG--INFY------------VPMSNKTG----------------------VVRS
+4=p             ----GTEG--KNFY------------VPMSNRTG----------------------LVRS
+5=p             ----GTEG--NNFY------------VPLSNRTG----------------------LVRS
+6==             ----QVPEFHEDFY------IPIP--LDINNLSA------------------------YS
+7==             ----KMSE--EEFY------------L-FKNISS----------------------V--G
+8=opsin,        ------------------------------------------------------------
+9==             ----STQS--SIFT------------YTNSNSTR-------------------------G
+10==            ----STQS--SIFT------------YTNSNSTR-------------------------G
+11==            ----TTRG--SVFT------------YTNTNNTR-------------------------G
+12==            ----TTRD--SVFT------------YTNSNNTR-------------------------G
+13==            ----SNSS------------------QAPPNGTP-------------------------G
+14==            SSLFGNVS--TALR-------------PEARLSA---E------TRLLGWNVPPEELRHI
+15==            SVL-GNVS--SVLR-------------PDARLSA---E------SRLLGWNVPPDELRHI
+16==            -PLCNASE--PPLR-------------PEAR-SSGNGD------LQFLGWNVPPDQIQYI
+17==            -ALCNASE--PPLR-------------PEARMSSGSDE------LQFLGWNVPPDQIQYI
+18==            ----NATG--PQMAY-----------YGAASMDFGYPE------GVSIVDFVRPEIKPYV
+19==            ----NVTG--PQMAF-----------YGSGAATFGYPE------GMTVADFVPDRVKHMV
+20==            AVAAAQLG--PHFA----------------PLS-----------NGSVVDKVTPDMAHLI
+21==            AVAAAQLG--PHFA----------------PLS-----------NGSVVDKVTPDMAHLI
+22==            AAVATQLG--PQFA----------------APS-----------NGSVVDKVTPDMAHLI
+23==            PFDLAHSG--PRFQ----------------AQSSG---------NGSVLDNVLPDMAHLV
+24==            PLAMALLG--PRFE----------------AQTGG---------NRSVLDNVLPDMAPLV
+25==            ----AVSG--PSYE----------------AFSYGGQARFN---NQTVVDKVPPDMLHLI
+26==            -----ANQ--LSYS----------------SLGWPYQP------NASVVDTMPKEMLYMI
+27==            ----ESTT--------------------LVNQTWWY--------NPTVD----------I
+28==            ----RDLR---------------------DNETWWY--------NPSIV----------V
+29==            DPVAGSWA--PHLL------------S---EVTASPAPTWDAPPDNASG-----------
+30==            ----------PHLL------------SGFLEVTASPAPTWDAPPDNVSG-----------
+31=p            ----------PHLL------------SGFLEVTASPAPTWDAPPDNVSG-----------
+32==            --------------------------PGQGNNTTSPPAPFETGGNTTGI-----------
+33=p            --------------------------FGQGNNTTASQEPFGTGGNVTSI-----------
+34==            QFINGSHS--SRSRD-----------NASANDT-----------SATNM----------T
+35=p            QFINGSHS--SRSRD-----------NASANDT-----------SATNM----------T
+36==            ----GAEG--QEELDWEALYLRLPLQNCSWNSTGWEPN-----WNVTVV----------P
+                                                                            
+
+1==             PYEYPQY------YLAEPWKYSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYIL
+2==             PFEQPQY------YLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYIL
+3==             PFEYPQY------YLAEPWKYRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYIL
+4=p             PFEYPQY------YLAEPWQFKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFIL
+5=p             PFEYPQY------YLAEPWQFKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFIL
+6==             PFLVPQD------HLGNQGIFMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYIL
+7==             PWDGPQY------HIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYIL
+8=opsin,        ------------------------------------------------------------
+9==             PFEGPNY------HIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWIL
+10==            PFEGPNY------HIAPRWVYHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWIL
+11==            PFEGPNY------HIAPRWVYNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWIL
+12==            PFEGPNY------HIAPRWVYNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWIL
+13==            PFDGPQWP-----YQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYIL
+14==            PEHWLTY------PEPPESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILV
+15==            PEHWLIY------PEPPESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILV
+16==            PEHWLTQ------LEPPASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFV
+17==            PEHWLTQ------LEPPASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFV
+18==            HQHWYNY------PPVNPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILV
+19==            LDHWYNY------PPVNPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLI
+20==            SPYWNQF------PAMDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLV
+21==            SPYWNQF------PAMDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLV
+22==            SPYWDQF------PAMDPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLV
+23==            NPYWSRF------APMDPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLV
+24==            NPHWSRF------APMDPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLV
+25==            DANWYQY------PPLNPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFV
+26==            HEHWYAF------PPMNPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLV
+27==            HPHWAKF------DPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFI
+28==            HPHWREF------DQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFI
+29==            ---------CGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLI
+30==            ---------CGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLI
+31=p            ---------CGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLI
+32==            -------------SDVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLI
+33=p            -------------SDVTFSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLI
+34==            DDRYWSL------TVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLI
+35=p            DDRYWSL------TVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLI
+36==            NTTWWQASAPFD-TPAALVRAAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLI
+                                                                            
+
+1==             LNLAMANLFMVLFG-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLA
+2==             LNLAVADLFMVFGG-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLA
+3==             VNLAVADLFMACFG-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLA
+4=p             VNLAVAGTIMVCFG-FTVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLA
+5=p             VNLAVAGAIMVCFG-FTVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLA
+6==             VNLSIANLFVAIFG-SPLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVA
+7==             VNVSFGGFLLCIFS-VFPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLA
+8=opsin,        ------DLAETVIA-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIIS
+9==             VNLAVADLAETVIA-STISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIIS
+10==            VNLAVADLAETVIA-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIIS
+11==            VNLAFVDLVETLVA-STISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIIS
+12==            VNLAVADLGETVIA-STISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIIS
+13==            VNLAVADLLVTLCG-SSVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILA
+14==            INLAFCDFMMM-VK-TPIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIA
+15==            INLAFCDFMMM-IK-TPIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIA
+16==            LNLAVFDLIMC-LK-APIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIG
+17==            LNLAVFDLIMC-LK-APIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIG
+18==            VNLALSDLIMLTTN-VPFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMIS
+19==            VNLALSDLIMLTTN-FPPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMIS
+20==            INLAISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMIS
+21==            INLAISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMIS
+22==            INLAISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMIS
+23==            LNLAFSDFCMMASQ-SPVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIA
+24==            LNLAFSDFCMMASQ-SPVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIA
+25==            INLAISNFLMMFCM-SPPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIA
+26==            VNLAFSDFCMMAFM-MPTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMIT
+27==            INLAMSDLSFSAINGFPLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMIS
+28==            INLAFSDFTFSLVNGFPLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMIS
+29==            VSLALADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVIS
+30==            VSLALADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVIS
+31=p            VSLALADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVIS
+32==            GSLAVTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIA
+33=p            GSLAVTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIA
+34==            LSLAVADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIA
+35=p            LSLAVADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIA
+36==            LSLAVADLLVACLV-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIA
+                      .                     :   :    * :                  : 
+
+1==             IERYIVICKPMGNF-RFGNTHAIMGVAFTWIMALAC-AAPPLVG-WS-----RYIPEGMQ
+2==             IERYVVVCKPMSNF-RFGENHAIMGVAFTWVMALAC-AAPPLVG-WS-----RYIPEGMQ
+3==             IERYIVVCKPMGNF-RFSATHAMMGIAFTWVMAFSC-AAPPLFG-WS-----RYMPEGMQ
+4=p             IERYIVVCKPMGSF-KFSSSHAFAGIAFTWVMALAC-AAPPLFG-WS-----RYIPEGMQ
+5=p             IERYIVVCKPMGSF-KFSSTHASAGIAFTWVMAMAC-AAPPLVG-WS-----RYIPEGIQ
+6==             FERWLVICKPLGNF-TFKTPHAIAGCILPWISALAA-SLPPLFG-WS-----RYIPEGLQ
+7==             FERYIVICKPFGNF-RFSSKHALTVVLATWTIGIGV-SIPPFFG-WS-----RFIPEGLQ
+8=opsin,        WERWLVVCKPFGNV-RFDAKLAIVGIAFSWIWAAVW-TAPPIFG-WS-----RYWPHGLK
+9==             WERWMVVCKPFGNV-RFDAKLAIVGIAFSWIWAAVW-TAPPIFG-WS-----RYWPHGLK
+10==            WERWLVVCKPFGNV-RFDAKLAIVGIAFSWIWSAVW-TAPPIFG-WS-----RYWPHGLK
+11==            WERWFVVCKPFGNI-KFDSKLAIIGIVFSWVWAWGW-SAPPIFG-WS-----RYWPHGLK
+12==            WERWFVVCKPFGNI-KFDGKLAVAGILFSWLWSCAW-TAPPIFG-WS-----RYWPHGLK
+13==            LERYVVVCKPLGDF-QFQRRHAVSGCAFTWGWALLW-SAPPLLG-WS-----SYVPEGLR
+14==            YDRFNVITRPMEG--KMTHGKAIAMIIFIYMYATPW-VVACYTETWG-----RFVPEGYL
+15==            YDRYNVITRPMEG--KMTHGKAIAMIIFIYLYATPW-VVACYTESWG-----RFVPEGYL
+16==            YDRYNVITKPMNR--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFWD-----RFVPEGYL
+17==            YDRYNVITKPMNR--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFWD-----RFVPEGYL
+18==            FDRYNIICNGFNGP-KLTTGKAVVFALISWVIAIGC-ALPPFFG-WG-----NYILEGIL
+19==            FDRYNIICNGFNGP-KLTQGKATFMCGLAWVISVGW-SLPPFFG-WG-----SYTLEGIL
+20==            LDRYQVIVKGMAGR-PMTIPLALGKM---------------------------YVPEGNL
+21==            LDRYQVIVKGMAGR-PMTIPLALGKIAYIWFMSSIW-CLAPAFG-WS-----RYVPEGNL
+22==            LDRYQVIVKGMAGR-PMTIPLALGKIAYIWFMSTIWCCLAPVFG-WS-----RYVPEGNL
+23==            FDRYNVIVKGINGT-PMTIKTSIMKILFIWMMAVFW-TVMPLIG-WS-----AYVPEGNL
+24==            FDRYNVIVKGINGT-PMTIKTSIMKIAFIWMMAVFW-TIMPLIG-WS-----SYVPEGNL
+25==            FDRYNVIVKGLSGK-PLSINGALIRIIAIWLFSLGW-TIAPMFG-WN-----RYVPEGNM
+26==            LDRYNVIVRGMAAA-PLTHKKATLLLLFVWIWSGGW-TILPFFG-WS-----RYVPEGNL
+27==            IDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVW-SVGPVFN-WG-----AYVPEGIL
+28==            IDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLW-AIGPIFG-WG-----AYTLEGVL
+29==            IDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKV
+30==            IDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKV
+31=p            IDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-WA-----QNVNDDKV
+32==            LDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDA
+33=p            LDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP---EDRSDPDA
+34==            MDRYWAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGT
+35=p            MDRYWAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGT
+36==            LDRYWAVTN-IDYIHASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLR
+                 :*:  :   :                                             .   
+
+1==             CSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQESA---
+2==             CSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESA---
+3==             CSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQESA---
+4=p             CSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDSA---
+5=p             CSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDSA---
+6==             CSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKAQADSA---
+7==             CSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESA---
+8=opsin,        TSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESE---
+9==             TSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESE---
+10==            TSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYLQVWLAIRAVAKQQKESE---
+11==            TSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQVWMAIRAVAAQQKESE---
+12==            TSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVWLAIRAVAAQQKESE---
+13==            TSCGPNWYTGGS--NNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEAD---
+14==            TSCTFDYLTDN--FDTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKM
+15==            TSCTFDYLTDN--FDTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKM
+16==            TSCSFDYLSDN--FDTRLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKKM
+17==            TSCSFDYLSDN--FDTRLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKKM
+18==            DSCSYDYLTQD--FNTFSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKKM
+19==            DSCSYDYFTRD--MNTITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKKM
+20==            TSCGIDYLERD--WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKM
+21==            TSCGIDYLERD--WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKM
+22==            TSCGIDYLERD--WNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKM
+23==            TACSIDYMTRM--WNPRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKKM
+24==            TACSIDYMTRQ--WNPRSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKKM
+25==            TACGTDYFNRG--LLSASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKKM
+26==            TSCTVDYLTKD--WSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKKM
+27==            TSCSFDYLSTD--PSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKRL
+28==            CNCSFDYISRD--STTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRL
+29==            CLISQDF----------GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPG---
+30==            CLISQDF----------GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPG---
+31=p            CLISQDF----------GYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPG---
+32==            CTISKDH----------GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKT
+33=p            CTISKDH----------GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKK
+34==            CIISQDK----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKA
+35=p            CIISQDK----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKA
+36==            CVVSQDV----------GYQIFATASSFYVPVLIILILYWRIYQTARKRIRRRRGATARG
+                     :                        *   :   *  :                  
+
+1==             ------------------------------------------------------------
+2==             ------------------------------------------------------------
+3==             ------------------------------------------------------------
+4=p             ------------------------------------------------------------
+5=p             ------------------------------------------------------------
+6==             ------------------------------------------------------------
+7==             ------------------------------------------------------------
+8=opsin,        ------------------------------------------------------------
+9==             ------------------------------------------------------------
+10==            ------------------------------------------------------------
+11==            ------------------------------------------------------------
+12==            ------------------------------------------------------------
+13==            ------------------------------------------------------------
+14==            NVE------------------SLRS-----------------------------------
+15==            NVD------------------SLRS-----------------------------------
+16==            NVE------------------SLRS-----------------------------------
+17==            NVE------------------SLRS-----------------------------------
+18==            NVS------------------TLRS-----------------------------------
+19==            NVT------------------NLRS-----------------------------------
+20==            NVK------------------SLRS-----------------------------------
+21==            NVK------------------SLRS-----------------------------------
+22==            NVK------------------SLRS-----------------------------------
+23==            NVK------------------SLRS-----------------------------------
+24==            NVK------------------SLRS-----------------------------------
+25==            NVA------------------SLRS-----------------------------------
+26==            NVA------------------SLRA-----------------------------------
+27==            NAK------------------ELRK-----------------------------------
+28==            NAK------------------ELRK-----------------------------------
+29==            -----------FPRVEPDSVIALNG-----------------------------------
+30==            -----------FPRVQPESVISLNG-----------------------------------
+31=p            -----------FPRVQPESVISLNG-----------------------------------
+32==            GADTRHGASPAPQPKK-----SVNGE--SGSRNWRLGVESKAGGALC-------------
+33=p            GAGTSLGTSSAPPPKK-----SLNGQ--PGSGDWRRCAENRAVGTPC-------------
+34==            RLKTEETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKK
+35=p            RLKTEETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKK
+36==            GVG---------------------------------------------PPP---------
+                                                                            
+
+1==             ------------------------------------------------------------
+2==             ------------------------------------------------------------
+3==             ------------------------------------------------------------
+4=p             ------------------------------------------------------------
+5=p             ------------------------------------------------------------
+6==             ------------------------------------------------------------
+7==             ------------------------------------------------------------
+8=opsin,        ------------------------------------------------------------
+9==             ------------------------------------------------------------
+10==            ------------------------------------------------------------
+11==            ------------------------------------------------------------
+12==            ------------------------------------------------------------
+13==            ------------------------------------------------------------
+14==            ------------------------------------------------------------
+15==            ------------------------------------------------------------
+16==            ------------------------------------------------------------
+17==            ------------------------------------------------------------
+18==            ------------------------------------------------------------
+19==            ------------------------------------------------------------
+20==            ------------------------------------------------------------
+21==            ------------------------------------------------------------
+22==            ------------------------------------------------------------
+23==            ------------------------------------------------------------
+24==            ------------------------------------------------------------
+25==            ------------------------------------------------------------
+26==            ------------------------------------------------------------
+27==            ------------------------------------------------------------
+28==            ------------------------------------------------------------
+29==            ---------------------------IVKLQKE-------------------VEECAN-
+30==            ---------------------------VVKLQKE-------------------VEECAN-
+31=p            ---------------------------VVKLQKE-------------------VEECAN-
+32==            -----------------------------------ANGAVRQGDDGAALEVIEVHRVGNS
+33=p            -----------------------------------TNGAVRQGDDEATLEVIEVHRVGNS
+34==            LPENANGVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAML-ERQCNNG
+35=p            LPENANGVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAML-ERQCNNG
+36==            VPAGGALVAGGGSGGIAAAVVAVIGRPLPTISETTTTGFTNVSSNNTSPE---KQSCANG
+                                                                            
+
+1==             -----------------------------------STQKAEKEVTRMVVLMVIGFLVCWV
+2==             -----------------------------------TTQKAEKEVTRMVIIMVIFFLICWL
+3==             -----------------------------------TTQKAEKEVTRMVILMVLGFMLAWT
+4=p             -----------------------------------STQKAEREVTKMVILMVFGFLIAWT
+5=p             -----------------------------------STQKAEREVTKMVILMVLGFLVAWT
+6==             -----------------------------------STQKAEREVTKMVVVMVLGFLVCWA
+7==             -----------------------------------TTQKAEREVSRMVVVMVGSFCVCYV
+8=opsin,        -----------------------------------STQKAEKEVTRMVVVMVLAFC----
+9==             -----------------------------------STQKAEKEVTRMVVVMVLAFCFCWG
+10==            -----------------------------------STQKAEKEVTRMVVVMIFAYCVCWG
+11==            -----------------------------------STQKAEREVSRMVVVMIVAFCICWG
+12==            -----------------------------------STQKAEKEVSRMVVVMIVAYCFCWG
+13==            -----------------------------------TTQRAEREVTRMVIVMVMAFLLCWL
+14==            -------------------------------NVDKNKETAEIRIAKAAITICFLFFCSWT
+15==            -------------------------------NVDKSKEAAEIRIAKAAITICFLFFASWT
+16==            -------------------------------NVDKSKETAEIRIAKAAITICFLFFVSWT
+17==            -------------------------------NVDKSKETAEIRIAKAAITICFLFFVSWT
+18==            --------------------------------NEADAQRAEIRIAKTALVNVSLWFICWT
+19==            --------------------------------NEAETQRAEIRIAKTALVNVSLWFICWT
+20==            --------------------------------SEDAEKSAEGKLAKVALVTITLWFMAWT
+21==            --------------------------------SEDAEKSAEGKLAKVALVTITLWFMAWT
+22==            --------------------------------SEDADKSAEGKLAKVALVTISLWFMAWT
+23==            --------------------------------SEDCDKSAEGKLAKVALTTISLWFMAWT
+24==            --------------------------------SEDCDKSAENKLAKVALTTISLWFMAWT
+25==            --------------------------------SENQNTSAECKLAKVALMTISLWFMAWT
+26==            -------------------------------NADQQKQSAECRLAKVAMMTVGLWFMAWT
+27==            ---------------------------------AQAGASAEMKLAKISMVIITQFMLSWS
+28==            ---------------------------------AQAGANAEMRLAKISIVIVSQFLLSWS
+29==            -----------------LSRLLKH------ERKNISIFKREQKAATTLGIIVGAFTVCWL
+30==            -----------------LSRLLKH------ERKNISIFKREQKAATTLGIIVGAFTVCWL
+31=p            -----------------LSRLLKH------ERKNISIFKREQKAATTLGIIVGAFTVCWL
+32==            KEHLPLPSEAG--PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWL
+33=p            KEHLPLPSESG--SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWL
+34==            KK-------------------ISSNDTPYSRTREKLELKRERKAARTLAIITGAFLICWL
+35=p            KK-------------------ISSNDTPYSRTREKLELKRERKAARTLAIITGAFLICWL
+36==            LEADPPTTGYGAVAAAYYPSLVRR------KPKEAADSKRERKAAKTLAIITGAFVACWL
+                                                        * .           :     
+
+1==             PYASVAFYIFT---HQGSD-FGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLC
+2==             PYASVAMYIFT---HQGSN-FGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLC
+3==             PYAVVAFWIFT---NKGAD-FTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTIC
+4=p             PYATVAAWIFF---NKGAD-FSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIF
+5=p             PYATVAAWIFF---NKGAA-FSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLF
+6==             PYASFSLWIVS---HRGEE-FDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMMKMVC
+7==             PYAAFAMYMVN---NRNHG-LDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIMKMVC
+8=opsin,        ------------------------------------------------------------
+9==             PYAFFACFAAA---NPGYP-FHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLF-
+10==            PYTFFACFAAA---NPGYA-FHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLF-
+11==            PYASFVSFAAA---NPGYA-FHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLF-
+12==            PYTFFACFAAA---NPGYA-FHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCILQLF-
+13==            PYSTFALVVAT---HKGII-IQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLLEMLC
+14==            PYGVMSLIGAF---GDKTL-LTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCP
+15==            PYGVMSLIGAF---GDKTL-LTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCP
+16==            PYGVMSLIGAF---GDKSL-LTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCP
+17==            PYGVMSLIGAF---GDKSL-LTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCP
+18==            PYALISLKGVM---GDTSG-ITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLP
+19==            PYAAITIQGLL---GNAEG-ITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLP
+20==            PYLVINCMGLF---KF-EG-LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCP
+21==            PYLVINCMGLF---KF-EG-LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCP
+22==            PYLVINCMGLF---KF-EG-LTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCP
+23==            PYLVICYFGLF---KI-DG-LTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCP
+24==            PYLIICYFGLF---KI-DG-LTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCP
+25==            PYLVINFSGIF---NL-VK-ISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFP
+26==            PYLIISWAGVF---SSGTR-LTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFP
+27==            PYAIIALLAQF---GPAEW-VTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFP
+28==            PYAVVALLAQF---GPLEW-VTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFP
+29==            PFFLLSTARPFICGTSCSC-IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQ
+30==            PFFLLSTARPFICGTSCSC-IPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQ
+31=p            PFFLLSTARPFICGTSCSC-IPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQ
+32==            PFFIVALVLPF---CESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIK
+33=p            PFFIVALVLPF---CESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIK
+34==            PFFIIALIGPF---VDPEG-IPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILF
+35=p            PFFIIALIGPF---VDPEG-IPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILF
+36==            PFFVLAILVPT---CDCE--VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLC
+                                                                            
+
+1==             C-GKNPLGDDE-SGA-STSKTEVSSVS-TSPV----------------------------
+2==             C-GKNPLGDDE-ASA-TASKTE------TSQV----------------------------
+3==             C-GKNPFGDEDVSSTVSQSKTEVSSVS-SSQV----------------------------
+4=p             C-GKNPLGDDE-SSTVSTSKTEVSS------V----------------------------
+5=p             C-GKNPLGDEE-SSTVSTSKTEVSS------V----------------------------
+6==             --GKN-IEEDE-AST-SSQVTQVSSVA-PEK-----------------------------
+7==             --GKA-MTDES-DTC-SSQKTEVSTVS-STQV----------------------------
+8=opsin,        ------------------------------------------------------------
+9==             --GKK-VDDGS-ELS-SASKTEVSSV---SSV----------------------------
+10==            --GKK-VDDGS-ELS-SASKTEVSSV---SSV----------------------------
+11==            --GKK-VDDGS-EAS-TTSRTEVSSVS-NSSV----------------------------
+12==            --GKK-VDDGS-EVS--TSRTEVSSVS-NSSV----------------------------
+13==            C-GYQPQRTGKASPGTPGPHADVTAAGLRNKV----------------------------
+14==            WLALNEKAPES-SAV-ASTST---TQE-PQQT----------------------------
+15==            WLAISEKAPES-RAA-ISTST---TQE-QQQT----------------------------
+16==            WLGVNEKSGEI-SSA-QSTTT---QEQ--QQT----------------------------
+17==            WLGVNEKSGEA-SSA-QSTTT---QEQ-TQQT----------------------------
+18==            WFCVHETETKS-NDD-SQSNS---TVA-Q-------------------------------
+19==            WFCVHEKDPND-VEE-NQSSN---TQT-Q-------------------------------
+20==            CCVFGKVDDGK-SSD-AQSQA-TASEA-E-------------------------------
+21==            CCVFGKVDDGK-SSD-AQSQA-TASEA-E-------------------------------
+22==            CCVFGKVDDGK-SSE-AQSQA-TTSEA-E-------------------------------
+23==            MCVFGNTDEPK-PDA-PASDTETTSEA-D-------------------------------
+24==            MCVCGTTDEPK-PDA-PPSDTETTSEA-E-------------------------------
+25==            SLACA-AEPSS-DAV-STTSG-TTTVT-DNEK----------------------------
+26==            SLACGSGESGS-DVK-SEASA-TTTME-EKPK----------------------------
+27==            WLLTCCQFDEK-ECE-DANDAEEEVVA-SER---GGESRDAAQMKEMMAMMQKMQAQQAA
+28==            WVLTCCQFDDK-ETE-DDKDAETEIPA-GESSD-AAPSADAAQMKEMMAMMQKMQQQQAA
+29==            --CQYRNINRKLSAA-GMHEALKLAER-PERPEFVLQNADYCRKKG--------------
+30==            --CQYRNINRKLSAA-GMHEALKLAER-PERSEFVLQNSDHCGKKG--------------
+31=p            --CQYRNINRKLSAA-GMHEALKLAER-PERSEFVLQNSDHCGKKG--------------
+32==            --CKFCR-----------------------------------------------------
+33=p            --CKFCR-----------------------------------------------------
+34==            --GKYRR-----------------------------------------------------
+35=p            --GKYRR-----------------------------------------------------
+36==            --GRRVR-RRR-------------------------------------------------
+                                                                            
+
+1==             ------------------------------------------------------------
+2==             ------------------------------------------------------------
+3==             ------------------------------------------------------------
+4=p             ------------------------------------------------------------
+5=p             ------------------------------------------------------------
+6==             ------------------------------------------------------------
+7==             ------------------------------------------------------------
+8=opsin,        ------------------------------------------------------------
+9==             ------------------------------------------------------------
+10==            ------------------------------------------------------------
+11==            ------------------------------------------------------------
+12==            ------------------------------------------------------------
+13==            ---------------------------------------MP-------------------
+14==            ------------------------------------------------------------
+15==            ------------------------------------------------------------
+16==            ------------------------------------------------------------
+17==            ------------------------------------------------------------
+18==            ------------------------------------------------------------
+19==            ------------------------------------------------------------
+20==            ------------------------------------------------------------
+21==            ------------------------------------------------------------
+22==            ------------------------------------------------------------
+23==            ------------------------------------------------------------
+24==            ------------------------------------------------------------
+25==            ------------------------------------------------------------
+26==            ------------------------------------------------------------
+27==            YQP---PPPPQGYPPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGA
+28==            YPPQGYAPPPQGYPPQGYPPQGY--PPQGYPPQGYPP---PPQGAPPQGAPP------AA
+29==            ------------------------------------------------------------
+30==            ------------------------------------------------------------
+31=p            ------------------------------------------------------------
+32==            ------------------------------------------------------------
+33=p            ------------------------------------------------------------
+34==            ------------------------------------------------------------
+35=p            ------------------------------------------------------------
+36==            ------------------------------------------------------------
+                                                                            
+
+1==             ---------SPA
+2==             ---------APA
+3==             ---------SPA
+4=p             ---------SPA
+5=p             ---------SPA
+6==             ------------
+7==             ---------GPN
+8=opsin,        ------------
+9==             ---------SPA
+10==            ---------SPA
+11==            ---------APA
+12==            ---------SPA
+13==            --------AHPV
+14==            ---------TAA
+15==            ---------TAA
+16==            ---------TAA
+17==            ---------SAA
+18==            ---------DKA
+19==            ---------EKS
+20==            ---------SKA
+21==            ---------SKA
+22==            ---------SKA
+23==            ---------SKA
+24==            ---------SKD
+25==            ---------SNA
+26==            --------IPEA
+27==            PPQGVDNQAYQA
+28==            PPQGVDNQAYQA
+29==            ---------HDS
+30==            ---------HDT
+31=p            ---------HDT
+32==            -----------Q
+33=p            -----------R
+34==            ---------GHR
+35=p            ---------GHR
+36==            ---------APQ
+                            
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_custom_parttree.aln	Wed Mar 20 07:34:52 2024 +0000
@@ -0,0 +1,504 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+MN-------------------GTE------GDNFYVPF----------------SNKTGL
+-----------ARSPYEYPQY-----YLAEPWK--------------------Y------
+------------------SALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNL
+AMANLFMVLFG-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIER
+YIVICKPMGN-FRFGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSC
+GPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---AAAAQQ------------------------------------ESASTQKAEKEVTRM
+VVLMVIGFLVCWVPYASVAFYIFT-HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMN
+KQFRNCMITTLC----C---GKNPLGD-DE--SGASTSKTEV------------------
+------------------------------------------------------------
+---SSVS-------TSPVSP-A----------
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+MN-------------------GTE------GPNFYVPF----------------SNITGV
+-----------VRSPFEQPQY-----YLAEPWQ--------------------F------
+------------------SMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNL
+AVADLFMVFGG-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIER
+YVVVCKPMSN-FRFGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSC
+GIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---AAAQQQ------------------------------------ESATTQKAEKEVTRM
+VIIMVIFFLICWLPYASVAMYIFT-HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMN
+KQFRNCMLTSLC----C---GKNPLGD-DE--ASATASKTE-------------------
+------------------------------------------------------------
+--------------TSQVAP-A----------
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+MN-------------------GTE------GINFYVPM----------------SNKTGV
+-----------VRSPFEYPQY-----YLAEPWK--------------------Y------
+------------------RLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNL
+AVADLFMACFG-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIER
+YIVVCKPMGN-FRFSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSC
+GPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---AAAQQQ------------------------------------ESATTQKAEKEVTRM
+VILMVLGFMLAWTPYAVVAFWIFT-NKGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMN
+KQFRNCMITTIC----C---GKNPFGD-EDVSSTVSQSKTEV------------------
+------------------------------------------------------------
+---SSVS-------SSQVSP-A----------
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+MN-------------------GTE------GKNFYVPM----------------SNRTGL
+-----------VRSPFEYPQY-----YLAEPWQ--------------------F------
+------------------KILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNL
+AVAGTIMVCFG-FTVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIER
+YIVVCKPMGS-FKFSSSHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSC
+GPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTV----KA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---AAAQQQ------------------------------------DSASTQKAEREVTKM
+VILMVFGFLIAWTPYATVAAWIFF-NKGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLN
+KQFRNCMLTTIF----C---GKNPLGD-DE-SSTVSTSKTEV------------------
+------------------------------------------------------------
+---SS------------VSP-A----------
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+MN-------------------GTE------GNNFYVPL----------------SNRTGL
+-----------VRSPFEYPQY-----YLAEPWQ--------------------F------
+------------------KLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNL
+AVAGAIMVCFG-FTVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIER
+YIVVCKPMGS-FKFSSTHASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSC
+GPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTV----KA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---AAAQQQ------------------------------------DSASTQKAEREVTKM
+VILMVLGFLVAWTPYATVAAWIFF-NKGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLN
+KQFRSCMLTTLF----C---GKNPLGD-EE-SSTVSTSKTEV------------------
+------------------------------------------------------------
+---SS------------VSP-A----------
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+MK-------------------QVPE----FHEDFYIPIPL------------DINNLSAY
+-------------SPFLVPQD-----HLGNQGI--------------------F------
+------------------MAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNL
+SIANLFVAIFG-SPLSFYSFFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFER
+WLVICKPLGN-FTFKTPHAIAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSC
+GPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITL----KL-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---AAKAQA------------------------------------DSASTQKAEREVTKM
+VVVMVLGFLVCWAPYASFSLWIVS-HRGE--EFDLRMATIPSCLSKASTVYNPVIYVLMN
+KQFRSCMM-KMV----C---GKN-IEE-DE--ASTSSQVTQV------------------
+------------------------------------------------------------
+---SS------------VAPEK----------
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+MR-------------------KMS------EEEFYL-----------------FKNISSV
+-------------GPWDGPQY-----HIAPVWA--------------------F------
+------------------YLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNV
+SFGGFLLCIFS-VFPVFVASCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFER
+YIVICKPFGN-FRFSSKHALTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSC
+GPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRAL----KA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---VAAQQQ------------------------------------ESATTQKAEREVSRM
+VVVMVGSFCVCYVPYAAFAMYMVN-NRNH--GLDLRLVTIPSFFSKSACIYNPIIYCFMN
+KQFQACIM-KMV----C---GKA-MTD-ES--DTCSSQKTEV------------------
+------------------------------------------------------------
+---STVS-------STQVGP-N----------
+>     8=opsin, greensensitive  human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---DLAETVIA-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWER
+WLVVCKPFGN-VRFDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSC
+GPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---VAKQQK------------------------------------ESESTQKAEKEVTRM
+VVVMVLAFC---------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDSYEDSTQ------SSIFTYTN----------------SNST--
+------------RGPFEGPNY-----HIAPRWV--------------------Y------
+------------------HLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNL
+AVADLAETVIA-STISVVNQVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWER
+WMVVCKPFGN-VRFDAKLAIVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSC
+GPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAI----RA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---VAKQQK------------------------------------ESESTQKAEKEVTRM
+VVVMVLAFCFCWGPYAFFACFAAA-NPGY--PFHPLMAALPAFFAKSATIYNPVIYVFMN
+RQFRNCILQLF---------GKK-VDD-GS--ELSSASKTEV------------------
+------------------------------------------------------------
+---SSV---------SSVSP-A----------
+>    10== Z68193   1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDSYEDSTQ------SSIFTYTN----------------SNST--
+------------RGPFEGPNY-----HIAPRWV--------------------Y------
+------------------HLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNL
+AVADLAETVIA-STISIVNQVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWER
+WLVVCKPFGN-VRFDAKLAIVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSC
+GPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYLQVWLAI----RA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---VAKQQK------------------------------------ESESTQKAEKEVTRM
+VVVMIFAYCVCWGPYTFFACFAAA-NPGY--AFHPLMAALPAYFAKSATIYNPVIYVFMN
+RQFRNCILQLF---------GKK-VDD-GS--ELSSASKTEV------------------
+------------------------------------------------------------
+---SSV---------SSVSP-A----------
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDD-DDTTR------GSVFTYTN----------------TNNT--
+------------RGPFEGPNY-----HIAPRWV--------------------Y------
+------------------NLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNL
+AFVDLVETLVA-STISVFNQIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWER
+WFVVCKPFGN-IKFDSKLAIIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSC
+GPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQVWMAI----RA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---VAAQQK------------------------------------ESESTQKAEREVSRM
+VVVMIVAFCICWGPYASFVSFAAA-NPGY--AFHPLAAALPAYFAKSATIYNPVIYVFMN
+RQFRNCIMQLF---------GKK-VDD-GS--EASTTSRTEV------------------
+------------------------------------------------------------
+---SSVS-------NSSVAP-A----------
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MA-AWEAAFAARRRHEE--EDTTR------DSVFTYTN----------------SNNT--
+------------RGPFEGPNY-----HIAPRWV--------------------Y------
+------------------NLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNL
+AVADLGETVIA-STISVINQIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWER
+WFVVCKPFGN-IKFDGKLAVAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSC
+GPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVWLAI----RA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---VAAQQK------------------------------------ESESTQKAEKEVSRM
+VVVMIVAYCFCWGPYTFFACFAAA-NPGY--AFHPLAAALPAYFAKSATIYNPIIYVFMN
+RQFRNCILQLF---------GKK-VDD-GS--EVST-SRTEV------------------
+------------------------------------------------------------
+---SSVS-------NSSVSP-A----------
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+MS-----------------SNSSQ------AP----------------------PNGT--
+------------PGPFDGPQW----PYQAPQST--------------------Y------
+------------------VGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNL
+AVADLLVTLCG-SSVSLSNNIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALER
+YVVVCKPLGD-FQFQRRHAVSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSC
+GPNWYTGGS--NNNSYILSLFVTCFVLPLSLILFSYTNLLLTL----RA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---AAAQQK------------------------------------EADTTQRAEREVTRM
+VIVMVMAFLLCWLPYSTFALVVAT-HKGI--IIQPVLASLPSYFSKTATVYNPIIYVFMN
+KQFQSCLLEMLC----CGYQPQR-TGK-AS--PGTPGPHADV------------------
+------------------------------------------------------------
+---TAAG------LRNKVMP-AH-------PV
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNV---------------SSSLFGNVST-ALRPEARLSA---ETRLLGW--------
+------------NVPPEELR------HIPEHWL-----------TYPEPPESMN------
+------------------YLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINL
+AFCDFMMMVK--TPIFIYNSFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDR
+FNVITRPMEG--KMTHGKAIAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSC
+TFDYLT--DNFDTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---LRDQAKK----------MNVESL----------------RSNVDKNKETAEIRIAKA
+AITICFLFFCSWTPYGVMSLIGAF-GDKT--LLTPGATMIPACACKMVACIDPFVYAISH
+PRYRMELQKRCP----WLALNEKAPE--SS-AVASTSTTQEP------------------
+------------------------------------------------------------
+---------------QQTTA-A----------
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNV---------------SSVL-GNVSS-VLRPDARLSA---ESRLLGW--------
+------------NVPPDELR------HIPEHWL-----------IYPEPPESMN------
+------------------YLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINL
+AFCDFMMMIK--TPIFIYNSFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDR
+YNVITRPMEG--KMTHGKAIAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSC
+TFDYLT--DNFDTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---LRDQAKK----------MNVDSL----------------RSNVDKSKEAAEIRIAKA
+AITICFLFFASWTPYGVMSLIGAF-GDKT--LLTPGATMIPACTCKMVACIDPFVYAISH
+PRYRMELQKRCP----WLAISEKAPE--SR-AAISTSTTQEQ------------------
+------------------------------------------------------------
+---------------QQTTA-A----------
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+ME---------------------PL-CNASEPPLRPEAR-SSGNGDLQFLGW--------
+------------NVPPDQIQ------YIPEHWL-----------TQLEPPASMH------
+------------------YMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNL
+AVFDLIMCLK--APIF--NSFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDR
+YNVITKPMNR--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSC
+SFDYLS--DNFDTRLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---LREQAKK----------MNVESL----------------RSNVDKSKETAEIRIAKA
+AITICFLFFVSWTPYGVMSLIGAF-GDKS--LLTQGATMIPACTCKLVACIDPFVYAISH
+PRYRLELQKRCP----WLGVNEKSGE--IS-SAQST-TTQEQ------------------
+------------------------------------------------------------
+---------------QQTTA-A----------
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MD---------------------AL-CNASEPPLRPEARMSSGSDELQFLGW--------
+------------NVPPDQIQ------YIPEHWL-----------TQLEPPASMH------
+------------------YMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNL
+AVFDLIMCLK--APIFIYNSFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDR
+YNVITKPMNR--NMTFTKAVIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSC
+SFDYLS--DNFDTRLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---LREQAKK----------MNVESL----------------RSNVDKSKETAEIRIAKA
+AITICFLFFVSWTPYGVMSLIGAF-GDKS--LLTPGATMIPACTCKLVACIEPFVYAISH
+PRYRMELQKRCP----WLGVNEKSGE--AS-SAQST-TTQEQ------------------
+------------------------------------------------------------
+--------------TQQTSA-A----------
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+MT-------------------------NATGPQMAYYGAASMD------FGYP-EGVSIV
+-----------DFVRPEIKP------YVHQHWY-----------NYPPVNPMWH------
+------------------YLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNL
+ALSDLIMLTTN-VPFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDR
+YNIICNGFNG-PKLTTGKAVVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSC
+SYDYLT--QDFNTFSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MRAQAKK----------MNVSTL----------------RS-NEADAQRAEIRIAKT
+ALVNVSLWFICWTPYALISLKGVM-GDTS--GITPLVSTLPALLAKSCSCYNPFVYAISH
+PKYRLAITQHLP----WFCVHETETKS-ND-DSQSNSTVAQ-------------------
+------------------------------------------------------------
+------------------DK-A----------
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+MA-------------------------NVTGPQMAFYGSGAAT------FGYP-EGMTVA
+-----------DFVPDRVKH------MVLDHWY-----------NYPPVNPMWH------
+------------------YLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNL
+ALSDLIMLTTN-FPPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDR
+YNIICNGFNG-PKLTQGKATFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSC
+SYDYFT--RDMNTITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MRAQAKK----------MNVTNL----------------RS-NEAETQRAEIRIAKT
+ALVNVSLWFICWTPYAAITIQGLL-GNAE--GITPLLTTLPALLAKSCSCYNPFVYAISH
+PKFRLAITQHLP----WFCVHEKDPND-VE-ENQSSNTQTQ-------------------
+------------------------------------------------------------
+------------------EK-S----------
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+ME-------------------SFAVAAAQLGPHFAPLS-----------------NGSVV
+-----------DKVTPDMAH------LISPYWN-----------QFPAMDPIWA------
+------------------KILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINL
+AISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDR
+YQVIVKGMAG-RPMTIPLALGKM---------------------------YVPEGNLTSC
+GIDYLE--RDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MREQAKK----------MNVKSL----------------RS-SEDAEKSAEGKLAKV
+ALVTITLWFMAWTPYLVINCMGLF-KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISH
+PKYRLALKEKCP----CCVFGKVDDGK-SS-DAQSQATASEA------------------
+------------------------------------------------------------
+---E--------------SK-A----------
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+ME-------------------SFAVAAAQLGPHFAPLS-----------------NGSVV
+-----------DKVTPDMAH------LISPYWN-----------QFPAMDPIWA------
+------------------KILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINL
+AISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDR
+YQVIVKGMAG-RPMTIPLALGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSC
+GIDYLE--RDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MREQAKK----------MNVKSL----------------RS-SEDAEKSAEGKLAKV
+ALVTITLWFMAWTPYLVINCMGLF-KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISH
+PKYRLALKEKCP----CCVFGKVDDGK-SS-DAQSQATASEA------------------
+------------------------------------------------------------
+---E--------------SK-A----------
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MD-------------------SFAAVATQLGPQFAAPS-----------------NGSVV
+-----------DKVTPDMAH------LISPYWD-----------QFPAMDPIWA------
+------------------KILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINL
+AISDFGIMITN-TPMMGINLYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDR
+YQVIVKGMAG-RPMTIPLALGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSC
+GIDYLE--RDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MREQAKK----------MNVKSL----------------RS-SEDADKSAEGKLAKV
+ALVTISLWFMAWTPYLVINCMGLF-KF-E--GLTPLNTIWGACFAKSAACYNPIVYGISH
+PKYRLALKEKCP----CCVFGKVDDGK-SS-EAQSQATTSEA------------------
+------------------------------------------------------------
+---E--------------SK-A----------
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSH--------------LPETPFDLAHSGPRFQAQSSG---------------NGSVL
+-----------DNVLPDMAH------LVNPYWS-----------RFAPMDPMMS------
+------------------KILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNL
+AFSDFCMMASQ-SPVMIINFYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDR
+YNVIVKGING-TPMTIKTSIMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTAC
+SIDYMT--RMWNPRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MREQAKK----------MNVKSL----------------RS-SEDCDKSAEGKLAKV
+ALTTISLWFMAWTPYLVICYFGLF-KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISH
+PKYRIVLKEKCP----MCVFGNTDEPKPDA-PASDTETTSEA------------------
+------------------------------------------------------------
+---D--------------SK-A----------
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSL--------------LPEPPLAMALLGPRFEAQTGG---------------NRSVL
+-----------DNVLPDMAP------LVNPHWS-----------RFAPMDPTMS------
+------------------KILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNL
+AFSDFCMMASQ-SPVMIINFYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDR
+YNVIVKGING-TPMTIKTSIMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTAC
+SIDYMT--RQWNPRSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKA-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MRDQAKK----------MNVKSL----------------RS-SEDCDKSAENKLAKV
+ALTTISLWFMAWTPYLIICYFGLF-KI-D--GLTPLTTIWGATFAKTSAVYNPIVYGISH
+PNDRLVLKEKCP----MCVCGTTDEPKPDA-PPSDTETTSEA------------------
+------------------------------------------------------------
+---E--------------SK-D----------
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+MI-------------------------AVSGPSYEAFSYGGQA-----RF----NNQTVV
+-----------DKVPPDMLH------LIDANWY-----------QYPPLNPMWH------
+------------------GILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINL
+AISNFLMMFCM-SPPMVINCYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDR
+YNVIVKGLSG-KPLSINGALIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTAC
+GTDYFN--RGLLSASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKN-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MREQAKK----------MNVASL----------------RS-SENQNTSAECKLAKV
+ALMTISLWFMAWTPYLVINFSGIF-NL-V--KISPLFTIWGSLFAKANAVYNPIVYGISH
+PKYRAALFAKFP----SLAC-AAEPSS-DA-VSTTSGTTTVT------------------
+------------------------------------------------------------
+---DNEK-----------SN-A----------
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+M---------------------------ANQLSYSSLGWPYQP------------NASVV
+-----------DTMPKEMLY------MIHEHWY-----------AFPPMNPLWY------
+------------------SILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNL
+AFSDFCMMAFM-MPTMTSNCFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDR
+YNVIVRGMAA-APLTHKKATLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSC
+TVDYLT--KDWSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQ-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---LREQAKK----------MNVASL----------------RANADQQKQSAECRLAKV
+AMMTVGLWFMAWTPYLIISWAGVF-SSGT--RLTPLATIWGSVFAKANSCYNPIVYGISH
+PRYKAALYQRFP----SLACGSGESGS-DV-KSEASATTTME------------------
+------------------------------------------------------------
+---EKPK----------IPE-A----------
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+MVESTTL------------VNQT--------------------------WWY---NPTVD
+---------------------------IHPHWA-----------KFDPIPDAVY------
+------------------YSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINL
+AMSDLSFSAINGFPLKTISAFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDR
+YNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSC
+SFDYLS--TDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKE-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MAAMAKR----------LNAKEL----------------R--KAQAGASAEMKLAKI
+SMVIITQFMLSWSPYAIIALLAQF-GPAE--WVTPYAAELPVLFAKASAIHNPIVYSVSH
+PKFREAIQTTFPWLLTCCQFDEKECED-AN-DAEEEVVASER--GGESRDAAQMKEMMAM
+MQKMQAQQAAYQPPPPPQGY--PPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAP
+PQVEAPQGAPPQGVDNQAYQ-A----------
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+MGRDLR-------------DNET--------------------------WWY---NPSIV
+---------------------------VHPHWR-----------EFDQVPDAVY------
+------------------YSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINL
+AFSDFTFSLVNGFPLMTISCFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDR
+YNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNC
+SFDYIS--RDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKE-----------
+------------------------------------------------------------
+------------------------------------------------------------
+---MAAMAKR----------LNAKEL----------------R--KAQAGANAEMRLAKI
+SIVIVSQFLLSWSPYAVVALLAQF-GPLE--WVTPYAAQLPVMFAKASAIHNPMIYSVSH
+PKFREAISQTFPWVLTCCQFDDKETED-DK-DAETEIPAGESSDAAPSADAAQMKEMMAM
+MQKMQQQQAAY----PPQGYAPPPQGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAP
+PQ-GAPPAAPPQGVDNQAYQ-A----------
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNS-------------SGRPDLY----GHLRSFLLP--EVG----------RGLPDL
+SPDGGADPVAGSWAPHLLS---EVTASPAPTWD------------APPDNASGC------
+-------GEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSL
+ALADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDR
+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDK--VC
+LIS--------QDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------
+---------PGF---------------------------------PRVEPDSVI------
+----------------ALNGIVK----------------------LQKEVEECAN-----
+---LSRLLKH--------------------------------ER-KNISIFKREQKAATT
+LGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTFLWLGYANSLINPFIYAFFN
+RDLRTTYRSLLQ--------CQYRNIN----RKLSAAGMHEA------------------
+-LKLA-------------------------------------------------------
+---ERPE------RPEFVLQNADYCRKKGHDS
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+M-----------------------------------------------------------
+--------------PHLLSGFLEVTASPAPTWD------------APPDNVSGC------
+-------GEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSL
+ALADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDR
+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDK--VC
+LIS--------QDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------
+---------PGF---------------------------------PRVQPESVI------
+----------------SLNGVVK----------------------LQKEVEECAN-----
+---LSRLLKH--------------------------------ER-KNISIFKREQKAATT
+LGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFN
+RDLRPTSRSLLQ--------CQYRNIN----RKLSAAGMHEA------------------
+-LKLA-------------------------------------------------------
+---ERPE------RSEFVLQNSDHCGKKGHDT
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+M-----------------------------------------------------------
+--------------PHLLSGFLEVTASPAPTWD------------APPDNVSGC------
+-------GEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSL
+ALADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDR
+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDK--VC
+LIS--------QDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF--------
+---------PGF---------------------------------PRVQPESVI------
+----------------SLNGVVK----------------------LQKEVEECAN-----
+---LSRLLKH--------------------------------ER-KNISIFKREQKAATT
+LGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFN
+RDLRTTYRSLLQ--------CQYRNIN----RKLSAAGMHEA------------------
+-LKLA-------------------------------------------------------
+---ERPE------RSEFVLQNSDHCGKKGHDT
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+M-DVLS-------------PGQ--------GNNTTSPPAPFETG----------GNTTGI
+-------------------------SDVTVSYQ---------------------------
+------------------VITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSL
+AVTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDR
+YWAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP--EDRSDPD---AC
+TIS--------KDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK-----------
+----------------------------TVKKVEKTGADTRHGASPAPQPKKSVNGESGS
+RNWRLGVESKAGGAL-CANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAP-
+----ASFERK-----------NERNA----------------EA-KRKMALARERKTVKT
+LGIIMGTFILCWLPFFIVALVLPF-CESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFN
+KDFQNAFKKIIK--------CKFCR-----------------------------------
+------------------------------------------------------------
+-------------------------------Q
+>    33=p A35181 serotonin receptor class 1A - rat
+M-DVFS-------------FGQ--------GNNTTASQEPFGTG----------GNVTSI
+-------------------------SDVTFSYQ---------------------------
+------------------VITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSL
+AVTDLMVSVLV-LPMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDR
+YWAITDPIDYVNKRTPRRAAALISLTWLIGFLI-SIPPMLG-WRTP--EDRSDPD---AC
+TIS--------KDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK-----------
+----------------------------TVRKVEKKGAGTSLGTSSAPPPKKSLNGQPGS
+GDWRRCAENRAVGTP-CTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESGSNSYAP-
+----ACLERK-----------NERNA----------------EA-KRKMALARERKTVKT
+LGIIMGTFILCWLPFFIVALVLPF-CESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFN
+KDFQNAFKKIIK--------CKFCR-----------------------------------
+------------------------------------------------------------
+-------------------------------R
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+M-ANFT-------------FGDLALDVARMGGLASTPSGLRSTG----------LTTPGL
+SPTG------------------LVTSDFNDSYGLTGQFINGSHSSRSRDNASAN-DTSAT
+NMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSL
+AVADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDR
+YWAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NN--DPDKTGTC
+IIS--------QDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLK
+TEETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKK--------
+--------NRAKKLPENANGVNSNSSSSERLKQIQIE-----------TAEAFANGCAEE
+AS-IAMLERQ-CNNGKKISSNDTPYS----------------RT-REKLELKRERKAART
+LAIITGAFLICWLPFFIIALIGPF-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFS
+PEFRSAFQKILF--------GKYRRG----------------------------------
+------------------------------------------------------------
+------------------------------HR
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+M-ANFT-------------FGDLALDVARMGGLASTPSGLRSTG----------LTTPGL
+SPTG------------------LVTSDFNDSYGLTGQFINGSHSSRSRDNASAN-DTSAT
+NMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSL
+AVADLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDR
+YWAVTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NN--DPDKTGTC
+IIS--------QDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLK
+TEETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKK--------
+--------NRAKKLPENANGVNSNSSSSERLKQIQIE-----------TAEAFANGCAEE
+AS-IAMLERQ-CNNGKKISSNDTPYS----------------RT-REKLELKRERKAART
+LAIITGAFLICWLPFFIIALIGPF-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFS
+PEFRSAFQKILF--------GKYRRG----------------------------------
+------------------------------------------------------------
+------------------------------HR
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+M-EG-A-------------EGQEELD----WEALYLRLPLQNCS----------WNSTGW
+EPNW------------------NVTVVPNTTWW----------------QASAPFDTPAA
+LVRA--------------AAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSL
+AVADLLVACLV-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDR
+YWAVTN-IDYIHASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDL--RC
+VVS--------QDVGYQIFATASSFYVPVLIILILYWRIYQTARKRIRR-----------
+----------------------------------RRGATARGGVGPPPVP----------
+-----------------AGGALVAGGGSGGIAAAVVAVIGRP---LPTISETTTTGFTNV
+SSNNTSPEKQSCANGLEA---DPPTTGYGAVAAAYYPSLVRRKP-KEAADSKRERKAAKT
+LAIITGAFVACWLPFFVLAILVPT-CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFS
+PEFRHAFQRLLC--------GRRVRRR----R----------------------------
+------------------------------------------------------------
+-----------------------------APQ
--- a/test-data/mafft_custom_result.aln	Tue Oct 31 15:48:53 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,458 +0,0 @@
-CLUSTAL format alignment by MAFFT F-INS-i (v7.455)
-
-
-1==             MN------------------------GTE--GDNFYVPFS--------NKTGL-ARSPYE
-2==             MN------------------------GTE--GPNFYVPFS--------NITGV-VRSPFE
-3==             MN------------------------GTE--GINFYVPMS--------NKTGV-VRSPFE
-4=p             MN------------------------GTE--GKNFYVPMS--------NRTGL-VRSPFE
-5=p             MN------------------------GTE--GNNFYVPLS--------NRTGL-VRSPFE
-6==             MK------------------------QVPEFHEDFYIPIP-------LDINNLSAYSPFL
-7==             MR------------------------KMS--EEEFYL------------FKNISSVGPWD
-8=opsin,        ------------------------------------------------------------
-9==             MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE
-10==            MAQQWSLQ-RLAGRHPQDS----YEDSTQ--SSIFTYTNS--------NS----TRGPFE
-11==            MTEAWNVAVFAARRSRDD------DDTTR--GSVFTYTNT--------NN----TRGPFE
-12==            MA-AWEAA-FAARRRHEE------EDTTR--DSVFTYTNS--------NN----TRGPFE
-13==            MS----------------------SNSSQ--------------AP--PNG----TPGPFD
-14==            MESG-NV-----------------------------------------SSSLFGNVSTAL
-15==            MEYH-NV------------------------------------------SSVLGNVSSVL
-16==            MEPLCNA------------------------------------------------SEPPL
-17==            MDALCNA------------------------------------------------SEPPL
-18==            MT-------------------------------------------------------NAT
-19==            MA-------------------------------------------------------NVT
-20==            ME-------------------------------------------------SFAVAAAQL
-21==            ME-------------------------------------------------SFAVAAAQL
-22==            MD-------------------------------------------------SFAAVATQL
-23==            MERS--------------------------------------------HLPETPFDLAHS
-24==            MERS--------------------------------------------LLPEPPLAMALL
-25==            MI-------------------------------------------------------AVS
-26==            M-----------------------------------------------------------
-27==            MVESTT------------------------------------------------------
-28==            MGRD--------------------------------------------------------
-29==            MM-----DVNSSGRPDLYGH-----------LRSFLLPEVGRGLPDLSPDGGADPVAGSW
-30==            M-----------------------------------------------------------
-31=p            M-----------------------------------------------------------
-32==            MD------VLSPGQ----------------------------------GNNTTSPPAPFE
-33=p            MD------VFSFGQ----------------------------------GNNTTASQEPFG
-34==            MA------NFTFGDLALDVARMGGLASTPS------------------GLRSTGLTTPGL
-35=p            MA------NFTFGDLALDVARMGGLASTPS------------------GLRSTGLTTPGL
-36==            ME-------GAEGQEELD-------------WEALYLRL---------PLQNCSWNSTGW
-                                                                            
-
-1==             YP----------------------------------------------------------
-2==             QP----------------------------------------------------------
-3==             YP----------------------------------------------------------
-4=p             YP----------------------------------------------------------
-5=p             YP----------------------------------------------------------
-6==             VP----------------------------------------------------------
-7==             GP----------------------------------------------------------
-8=opsin,        ------------------------------------------------------------
-9==             GP----------------------------------------------------------
-10==            GP----------------------------------------------------------
-11==            GP----------------------------------------------------------
-12==            GP----------------------------------------------------------
-13==            GP----------------------------------------------------------
-14==            RPEARL----------------------SAETRLLGWNVPPEELRHIPEHWL--------
-15==            RPDARL----------------------SAESRLLGWNVPPDELRHIPEHWL--------
-16==            RPEAR-SSG-------------------NGDLQFLGWNVPPDQIQYIPEHWL--------
-17==            RPEARMSSG-------------------SDELQFLGWNVPPDQIQYIPEHWL--------
-18==            GPQMAYYGAASMDFG-------------YPEGVSIVDFVRPEIKPYVHQHWY--------
-19==            GPQMAFYGSGAATFG-------------YPEGMTVADFVPDRVKHMVLDHWY--------
-20==            GPHFAPLS-----------------------NGSVVDKVTPDMAHLISPYWN--------
-21==            GPHFAPLS-----------------------NGSVVDKVTPDMAHLISPYWN--------
-22==            GPQFAAPS-----------------------NGSVVDKVTPDMAHLISPYWD--------
-23==            GPRFQAQSSG---------------------NGSVLDNVLPDMAHLVNPYWS--------
-24==            GPRFEAQTGG---------------------NRSVLDNVLPDMAPLVNPHWS--------
-25==            GPSYEAFSYG--GQA-------------RFNNQTVVDKVPPDMLHLIDANWY--------
-26==            -ANQLSYSSL--GWP-------------YQPNASVVDTMPKEMLYMIHEHWY--------
-27==            ----------LVNQT-------------WWYNPTV----------DIHPHWA--------
-28==            ---------LRDNET-------------WWYNPSI----------VVHPHWR--------
-29==            APHLLS-----------------------------------EVTASPAPTWDAPPDNASG
-30==            -PHLLSGF--------------------------------LEVTASPAPTWDAPPDNVSG
-31=p            -PHLLSGF--------------------------------LEVTASPAPTWDAPPDNVSG
-32==            TG--------------------------------------GNTTGI--------------
-33=p            TG--------------------------------------GNVTSI--------------
-34==            SPTGLVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTD--DRYWSL-------
-35=p            SPTGLVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTD--DRYWSL-------
-36==            EPNW-------------------------------------NVTVVPNTTWWQ-------
-                                                                            
-
-1==             -----QY-YLAEPWKYSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAM
-2==             -----QY-YLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAV
-3==             -----QY-YLAEPWKYRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAV
-4=p             -----QY-YLAEPWQFKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAV
-5=p             -----QY-YLAEPWQFKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAV
-6==             -----QD-HLGNQGIFMAMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSI
-7==             -----QY-HIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSF
-8=opsin,        ------------------------------------------------------------
-9==             -----NY-HIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAV
-10==            -----NY-HIAPRWVYHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAV
-11==            -----NY-HIAPRWVYNLVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAF
-12==            -----NY-HIAPRWVYNLTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAV
-13==            -----QWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAV
-14==            -----TY-PEPPESMNYLLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAF
-15==            -----IY-PEPPESMNYLLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAF
-16==            -----TQ-LEPPASMHYMLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAV
-17==            -----TQ-LEPPASMHYMLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAV
-18==            -----NY-PPVNPMWHYLLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLAL
-19==            -----NY-PPVNPMWHYLLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLAL
-20==            -----QF-PAMDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAI
-21==            -----QF-PAMDPIWAKILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAI
-22==            -----QF-PAMDPIWAKILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAI
-23==            -----RF-APMDPMMSKILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAF
-24==            -----RF-APMDPTMSKILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAF
-25==            -----QY-PPLNPMWHGILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAI
-26==            -----AF-PPMNPLWYSILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAF
-27==            -----KF-DPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAM
-28==            -----EF-DQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAF
-29==            CGEQINY----GRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLAL
-30==            CGEQINY----GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLAL
-31=p            CGEQINY----GRVEKVVIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLAL
-32==            SDVTVSY--------QVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAV
-33=p            SDVTFSY--------QVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAV
-34==            TVYSHEH--------LVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAV
-35=p            TVYSHEH--------LVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAV
-36==            --ASAPFDTPAALVRAAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAV
-                                                                            
-
-1==             ANLFMVLFG-FTVTMYTSMNG-YFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYI
-2==             ADLFMVFGG-FTTTLYTSLHG-YFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYV
-3==             ADLFMACFG-FTVTFYTAWNG-YFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYI
-4=p             AGTIMVCFG-FTVTFYTAING-YFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYI
-5=p             AGAIMVCFG-FTVTFYTAING-YFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYI
-6==             ANLFVAIFG-SPLSFYSFFNR-YFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWL
-7==             GGFLLCIFS-VFPVFVASCNG-YFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYI
-8=opsin,        -DLAETVIA-STISIVNQVSG-YFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWL
-9==             ADLAETVIA-STISVVNQVYG-YFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWM
-10==            ADLAETVIA-STISIVNQVSG-YFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWL
-11==            VDLVETLVA-STISVFNQIFG-YFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWF
-12==            ADLGETVIA-STISVINQISG-YFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWF
-13==            ADLLVTLCG-SSVSLSNNING-FFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYV
-14==            CDFMMMVK--TPIFIYNSFHQ-GYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFN
-15==            CDFMMMIK--TPIFIYNSFHQ-GYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYN
-16==            FDLIMCLK--APIF--NSFHR-GFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYN
-17==            FDLIMCLK--APIFIYNSFHR-GFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYN
-18==            SDLIMLTTN-VPFFTYNCFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYN
-19==            SDLIMLTTN-FPPFCYNCFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYN
-20==            SDFGIMITN-TPMMGINLYFE-TWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQ
-21==            SDFGIMITN-TPMMGINLYFE-TWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQ
-22==            SDFGIMITN-TPMMGINLYFE-TWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQ
-23==            SDFCMMASQ-SPVMIINFYYE-TWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYN
-24==            SDFCMMASQ-SPVMIINFYYE-TWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYN
-25==            SNFLMMFCM-SPPMVINCYYE-TWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYN
-26==            SDFCMMAFM-MPTMTSNCFAE-TWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYN
-27==            SDLSFSAINGFPLKTISAFMK-KWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYN
-28==            SDFTFSLVNGFPLMTISCFLK-KWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYN
-29==            ADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYL
-30==            ADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYL
-31=p            ADLSVAVAV-MPFVSVTDLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYL
-32==            TDLMVSVLV-LPMAALYQVLN-KWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYW
-33=p            TDLMVSVLV-LPMAALYQVLN-KWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYW
-34==            ADLMVAVLV-MPLSVVSEISK-VWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYW
-35=p            ADLMVAVLV-MPLSVVSEISK-VWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYW
-36==            ADLLVACLV-MPLGAVYEVVQ-RWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYW
-                 .                     :   :    * :                  :  :*: 
-
-1==             VICKPMGNFR-FGNTHAIMGVAFTWIMALACA-APPLV-GWSRYIPEGMQCSCGPDYYTL
-2==             VVCKPMSNFR-FGENHAIMGVAFTWVMALACA-APPLV-GWSRYIPEGMQCSCGIDYYTL
-3==             VVCKPMGNFR-FSATHAMMGIAFTWVMAFSCA-APPLF-GWSRYMPEGMQCSCGPDYYTH
-4=p             VVCKPMGSFK-FSSSHAFAGIAFTWVMALACA-APPLF-GWSRYIPEGMQCSCGPDYYTL
-5=p             VVCKPMGSFK-FSSTHASAGIAFTWVMAMACA-APPLV-GWSRYIPEGIQCSCGPDYYTL
-6==             VICKPLGNFT-FKTPHAIAGCILPWISALAAS-LPPLF-GWSRYIPEGLQCSCGPDWYTT
-7==             VICKPFGNFR-FSSKHALTVVLATWTIGIGVS-IPPFF-GWSRFIPEGLQCSCGPDWYTV
-8=opsin,        VVCKPFGNVR-FDAKLAIVGIAFSWIWAAVWT-APPIF-GWSRYWPHGLKTSCGPDVFSG
-9==             VVCKPFGNVR-FDAKLAIVGIAFSWIWAAVWT-APPIF-GWSRYWPHGLKTSCGPDVFSG
-10==            VVCKPFGNVR-FDAKLAIVGIAFSWIWSAVWT-APPIF-GWSRYWPHGLKTSCGPDVFSG
-11==            VVCKPFGNIK-FDSKLAIIGIVFSWVWAWGWS-APPIF-GWSRYWPHGLKTSCGPDVFSG
-12==            VVCKPFGNIK-FDGKLAVAGILFSWLWSCAWT-APPIF-GWSRYWPHGLKTSCGPDVFSG
-13==            VVCKPLGDFQ-FQRRHAVSGCAFTWGWALLWS-APPLL-GWSSYVPEGLRTSCGPNWYTG
-14==            VITRPMEGK--MTHGKAIAMIIFIYMYATPWV-VACYTETWGRFVPEGYLTSCTFDYLTD
-15==            VITRPMEGK--MTHGKAIAMIIFIYLYATPWV-VACYTESWGRFVPEGYLTSCTFDYLTD
-16==            VITKPMNRN--MTFTKAVIMNIIIWLYCTPWV-VLPLTQFWDRFVPEGYLTSCSFDYLSD
-17==            VITKPMNRN--MTFTKAVIMNIIIWLYCTPWV-VLPLTQFWDRFVPEGYLTSCSFDYLSD
-18==            IICNGFNGPK-LTTGKAVVFALISWVIAIGCA-LPPFF-GWGNYILEGILDSCSYDYLTQ
-19==            IICNGFNGPK-LTQGKATFMCGLAWVISVGWS-LPPFF-GWGSYTLEGILDSCSYDYFTR
-20==            VIVKGMAGRP-MTIPLALGKM----------------------YVPEGNLTSCGIDYLER
-21==            VIVKGMAGRP-MTIPLALGKIAYIWFMSSIWC-LAPAF-GWSRYVPEGNLTSCGIDYLER
-22==            VIVKGMAGRP-MTIPLALGKIAYIWFMSTIWCCLAPVF-GWSRYVPEGNLTSCGIDYLER
-23==            VIVKGINGTP-MTIKTSIMKILFIWMMAVFWT-VMPLI-GWSAYVPEGNLTACSIDYMTR
-24==            VIVKGINGTP-MTIKTSIMKIAFIWMMAVFWT-IMPLI-GWSSYVPEGNLTACSIDYMTR
-25==            VIVKGLSGKP-LSINGALIRIIAIWLFSLGWT-IAPMF-GWNRYVPEGNMTACGTDYFNR
-26==            VIVRGMAAAP-LTHKKATLLLLFVWIWSGGWT-ILPFF-GWSRYVPEGNLTSCTVDYLTK
-27==            VIGRPMAASKKMSHRRAFLMIIFVWMWSIVWS-VGPVF-NWGAYVPEGILTSCSFDYLST
-28==            VIGRPMAASKKMSHRRAFIMIIFVWLWSVLWA-IGPIF-GWGAYTLEGVLCNCSFDYISR
-29==            GITRPLTYPVRQNGKCMAKMILSVWLLSASIT-LPPLF-GWAQNVNDDKVC-----LISQ
-30==            GITRPLTYPVRQNGKCMAKMILSVWLLSASIT-LPPLF-GWAQNVNDDKVC-----LISQ
-31=p            GITRPLTYPVRQNGKCMAKMILSVWLLSASIT-LPPLF-GWAQNVNDDKVC-----LISQ
-32==            AITDPIDYVNKRTPRRAAALISLTWLIGFLIS-IPPML-GWRTPEDRSDPDAC---TISK
-33=p            AITDPIDYVNKRTPRRAAALISLTWLIGFLIS-IPPML-GWRTPEDRSDPDAC---TISK
-34==            AVTS-IDYIRRRSARRILLMIMVVWIVALFIS-IPPLF-GWRD--PNNDPDKTGTCIISQ
-35=p            AVTS-IDYIRRRSARRILLMIMVVWIVALFIS-IPPLF-GWRD--PNNDPDKTGTCIISQ
-36==            AVTN-IDYIHASTAKRVGMMIACVWTVSFFVC-IAQLL-GWKDPDWNQRVSEDLRCVVSQ
-                 :   :                                                      
-
-1==             NPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQE---------------
-2==             KPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQE---------------
-3==             NPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQE---------------
-4=p             NPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQD---------------
-5=p             NPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQD---------------
-6==             NNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKAQAD---------------
-7==             GTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQE---------------
-8=opsin,        SSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKE---------------
-9==             SSYPGVQSYMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKE---------------
-10==            SSYPGVQSYMIVLMVTCCIIPLAIIMLCYLQVWLAIRAVAKQQKE---------------
-11==            SVELGCQSFMLTLMITCCFLPLFIIIVCYLQVWMAIRAVAAQQKE---------------
-12==            SSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVWLAIRAVAAQQKE---------------
-13==            GS--NNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKE---------------
-14==            NF--DTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKMNVESLRSNV-
-15==            NF--DTRLFVACIFFFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKKMNVDSLRSNV-
-16==            NF--DTRLFVGTIFFFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKKMNVESLRSNV-
-17==            NF--DTRLFVGTIFLFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKKMNVESLRSNV-
-18==            DF--NTFSYNIFIFVFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKKMNVSTLRSN--
-19==            DM--NTITYNICIFIFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKKMNVTNLRSN--
-20==            DW--NPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLRSS--
-21==            DW--NPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLRSS--
-22==            DW--NPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSLRSS--
-23==            MW--NPRSYLITYSLFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKKMNVKSLRSS--
-24==            QW--NPRSYLITYSLFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKKMNVKSLRSS--
-25==            GL--LSASYLVCYGIWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKKMNVASLRSS--
-26==            DW--SSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKKMNVASLRANA-
-27==            DP--STRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKRLNAKELRKA--
-28==            DS--TTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNAKELRKA--
-29==            D-----FGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFP--------------
-30==            D-----FGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFP--------------
-31=p            D-----FGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFP--------------
-32==            D-----HGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASP
-33=p            D-----HGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGTSLGTSS
-34==            D-----KGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLV
-35=p            D-----KGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLV
-36==            D-----VGYQIFATASSFYVPVLIILILYWRIYQTARKRIRRRRGA-------TARGGVG
-                                    *   :   *  :                            
-
-1==             ------------------------------------------------------------
-2==             ------------------------------------------------------------
-3==             ------------------------------------------------------------
-4=p             ------------------------------------------------------------
-5=p             ------------------------------------------------------------
-6==             ------------------------------------------------------------
-7==             ------------------------------------------------------------
-8=opsin,        ------------------------------------------------------------
-9==             ------------------------------------------------------------
-10==            ------------------------------------------------------------
-11==            ------------------------------------------------------------
-12==            ------------------------------------------------------------
-13==            ------------------------------------------------------------
-14==            ------------------------------------------------------------
-15==            ------------------------------------------------------------
-16==            ------------------------------------------------------------
-17==            ------------------------------------------------------------
-18==            ------------------------------------------------------------
-19==            ------------------------------------------------------------
-20==            ------------------------------------------------------------
-21==            ------------------------------------------------------------
-22==            ------------------------------------------------------------
-23==            ------------------------------------------------------------
-24==            ------------------------------------------------------------
-25==            ------------------------------------------------------------
-26==            ------------------------------------------------------------
-27==            ------------------------------------------------------------
-28==            ------------------------------------------------------------
-29==            GFPRVE--------------------------------PDSVI----------ALNGIVK
-30==            GFPRVQ--------------------------------PESVI----------SLNGVVK
-31=p            GFPRVQ--------------------------------PESVI----------SLNGVVK
-32==            A-PQPKKS-VNGESGSRNWRLGVESKAGGAL-----C-----------------ANGAVR
-33=p            A-PPPKKS-LNGQPGSGDWRRCAENRAVGTP-----C-----------------TNGAVR
-34==            ASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGV--
-35=p            ASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGV--
-36==            PPPVPAGGALVAGGGSGGIAAAVVAVIGR---------PLPTISET-------TTTGFTN
-                                                                            
-
-1==             ------------------------------------------------------------
-2==             ------------------------------------------------------------
-3==             ------------------------------------------------------------
-4=p             ------------------------------------------------------------
-5=p             ------------------------------------------------------------
-6==             ------------------------------------------------------------
-7==             ------------------------------------------------------------
-8=opsin,        ------------------------------------------------------------
-9==             ------------------------------------------------------------
-10==            ------------------------------------------------------------
-11==            ------------------------------------------------------------
-12==            ------------------------------------------------------------
-13==            ------------------------------------------------------------
-14==            ------------------------------------------------------------
-15==            ------------------------------------------------------------
-16==            ------------------------------------------------------------
-17==            ------------------------------------------------------------
-18==            ------------------------------------------------------------
-19==            ------------------------------------------------------------
-20==            ------------------------------------------------------------
-21==            ------------------------------------------------------------
-22==            ------------------------------------------------------------
-23==            ------------------------------------------------------------
-24==            ------------------------------------------------------------
-25==            ------------------------------------------------------------
-26==            ------------------------------------------------------------
-27==            ------------------------------------------------------------
-28==            ------------------------------------------------------------
-29==            -------------LQKEVEEC-AN------------------LSRLLKHER---------
-30==            -------------LQKEVEEC-AN------------------LSRLLKHER---------
-31=p            -------------LQKEVEEC-AN------------------LSRLLKHER---------
-32==            QGDDGAALEV-----IEVHRV-GNSKEHLPLPSEAGP--TPCAPASFERKNERN------
-33=p            QGDDEATLEV-----IEVHRV-GNSKEHLPLPSESGS--NSYAPACLERKNERN------
-34==            -NSNSSSSERLKQIQIETAEAFANGC------------AEEASIAMLERQCNNGKKISSN
-35=p            -NSNSSSSERLKQIQIETAEAFANGC------------AEEASIAMLERQCNNGKKISSN
-36==            VSSNNTSP--------EKQSC-ANGLEADPPTTGYGAVAAAYYPSLVRRKP---------
-                                                                            
-
-1==             --------SASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT--HQGSDFGAT-FM
-2==             --------SATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFT--HQGSNFGPI-FM
-3==             --------SATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT--NKGADFTAT-LM
-4=p             --------SASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFF--NKGADFSAK-FM
-5=p             --------SASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFF--NKGAAFSAQ-FM
-6==             --------SASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVS--HRGEEFDLR-MA
-7==             --------SATTQKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN--NRNHGLDLR-LV
-8=opsin,        --------SESTQKAEKEVTRMVVVMVLAFC-----------------------------
-9==             --------SESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA--NPGYPFHPL-MA
-10==            --------SESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA--NPGYAFHPL-MA
-11==            --------SESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAA--NPGYAFHPL-AA
-12==            --------SESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA--NPGYAFHPL-AA
-13==            --------ADTTQRAEREVTRMVIVMVMAFLLCWLPYSTFALVVAT--HKGIIIQPV-LA
-14==            --------DKNKETAEIRIAKAAITICFLFFCSWTPYGVMSLIGAF--GDKTLLTPG-AT
-15==            --------DKSKEAAEIRIAKAAITICFLFFASWTPYGVMSLIGAF--GDKTLLTPG-AT
-16==            --------DKSKETAEIRIAKAAITICFLFFVSWTPYGVMSLIGAF--GDKSLLTQG-AT
-17==            --------DKSKETAEIRIAKAAITICFLFFVSWTPYGVMSLIGAF--GDKSLLTPG-AT
-18==            --------EADAQRAEIRIAKTALVNVSLWFICWTPYALISLKGVM--GDTSGITPL-VS
-19==            --------EAETQRAEIRIAKTALVNVSLWFICWTPYAAITIQGLL--GNAEGITPL-LT
-20==            --------EDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLF--KF-EGLTPL-NT
-21==            --------EDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLF--KF-EGLTPL-NT
-22==            --------EDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMGLF--KF-EGLTPL-NT
-23==            --------EDCDKSAEGKLAKVALTTISLWFMAWTPYLVICYFGLF--KI-DGLTPL-TT
-24==            --------EDCDKSAENKLAKVALTTISLWFMAWTPYLIICYFGLF--KI-DGLTPL-TT
-25==            --------ENQNTSAECKLAKVALMTISLWFMAWTPYLVINFSGIF--NL-VKISPL-FT
-26==            --------DQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVF--SSGTRLTPL-AT
-27==            --------Q-AGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQF--GPAEWVTPY-AA
-28==            --------Q-AGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQF--GPLEWVTPY-AA
-29==            -------KNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVE
-30==            -------KNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVE
-31=p            -------KNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSCIPLWVE
-32==            ----AEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CESSCHMPTL-LG
-33=p            ----AEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CESSCHMPAL-LG
-34==            DTPYSRTREKLELKRERKAARTLAIITGAFLICWLPFFIIALIGPF--VDPEGIPPF-AR
-35=p            DTPYSRTREKLELKRERKAARTLAIITGAFLICWLPFFIIALIGPF--VDPEGIPPF-AR
-36==            -------KEAADSKRERKAAKTLAIITGAFVACWLPFFVLAILVPT-CD--CEVSPV-LT
-                               * .           :                              
-
-1==             TLPAFFAKSSALYNPVIYILMNKQFRNCMITTL-----CC-----GKNPLGDDE-SGA-S
-2==             TLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSL-----CC-----GKNPLGDDE-ASA-T
-3==             AVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTI-----CC-----GKNPFGDEDVSSTVS
-4=p             AIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTI-----FC-----GKNPLGDDE-SSTVS
-5=p             AIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTL-----FC-----GKNPLGDEE-SSTVS
-6==             TIPSCLSKASTVYNPVIYVLMNKQFRSCMMK-M-----VC-----GKN-IEEDE-AST-S
-7==             TIPSFFSKSACIYNPIIYCFMNKQFQACIMK-M-----VC-----GKA-MTDES-DTC-S
-8=opsin,        ------------------------------------------------------------
-9==             ALPAFFAKSATIYNPVIYVFMNRQFRNCILQ-L-----F------GKK-VDDGS-ELS-S
-10==            ALPAYFAKSATIYNPVIYVFMNRQFRNCILQ-L-----F------GKK-VDDGS-ELS-S
-11==            ALPAYFAKSATIYNPVIYVFMNRQFRNCIMQ-L-----F------GKK-VDDGS-EAS-T
-12==            ALPAYFAKSATIYNPIIYVFMNRQFRNCILQ-L-----F------GKK-VDDGS-EVS-T
-13==            SLPSYFSKTATVYNPIIYVFMNKQFQSCLLEML-----CC-----GYQPQRTGKASPGTP
-14==            MIPACACKMVACIDPFVYAISHPRYRMELQKRCPW---LALN---EK----APE-SSA-V
-15==            MIPACTCKMVACIDPFVYAISHPRYRMELQKRCPW---LAIS---EK----APE-SRA-A
-16==            MIPACTCKLVACIDPFVYAISHPRYRLELQKRCPW---LGVN---EK----SGE-ISS-A
-17==            MIPACTCKLVACIEPFVYAISHPRYRMELQKRCPW---LGVN---EK----SGE-ASS-A
-18==            TLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPW---FCVH---ET----ETK-SND-D
-19==            TLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPW---FCVH---EK----DPN-DVE-E
-20==            IWGACFAKSAACYNPIVYGISHPKYRLALKEKCP----CCVF---GKV--DDGK-SSD-A
-21==            IWGACFAKSAACYNPIVYGISHPKYRLALKEKCP----CCVF---GKV--DDGK-SSD-A
-22==            IWGACFAKSAACYNPIVYGISHPKYRLALKEKCP----CCVF---GKV--DDGK-SSE-A
-23==            IWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCP----MCVF---GNT--DEPK-PDA-P
-24==            IWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCP----MCVC---GTT--DEPK-PDA-P
-25==            IWGSLFAKANAVYNPIVYGISHPKYRAALFAKFP----SLAC---AA----EPS-SDA-V
-26==            IWGSVFAKANSCYNPIVYGISHPRYKAALYQRFP----SLAC---GS---GESG-SDV-K
-27==            ELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQF---DEK--ECED-AND-A
-28==            QLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQF---DDK--ETED-DKD-A
-29==            RTFLWLGYANSLINPFIYAFFNRDLRTTYRSLL-----QCQYRNINRKL------SAAGM
-30==            RTCLWLGYANSLINPFIYAFFNRDLRPTSRSLL-----QCQYRNINRKL------SAAGM
-31=p            RTCLWLGYANSLINPFIYAFFNRDLRTTYRSLL-----QCQYRNINRKL------SAAGM
-32==            AIINWLGYSNSLLNPVIYAYFNKDFQNAFKKII-----KCKF---CRQ------------
-33=p            AIINWLGYSNSLLNPVIYAYFNKDFQNAFKKII-----KCKF---CRR------------
-34==            SFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKYR-RGHR------------
-35=p            SFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKIL-----FGKYR-RGHR------------
-36==            SLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLL------CGRRVRRRR------------
-                                                                            
-
-1==             TSKTEVSSVSTS------------------------------------------------
-2==             ASKTETSQVA--------------------------------------------------
-3==             QSKTEVSSVSSS------------------------------------------------
-4=p             TSKTEVSSVS--------------------------------------------------
-5=p             TSKTEVSSVS--------------------------------------------------
-6==             SQVTQVSSVA--------------------------------------------------
-7==             SQKTEVSTVSST------------------------------------------------
-8=opsin,        ------------------------------------------------------------
-9==             ASKTEVSSVS--------------------------------------------------
-10==            ASKTEVSSVS--------------------------------------------------
-11==            TSRTEVSSVSNS------------------------------------------------
-12==            -SRTEVSSVSNS------------------------------------------------
-13==            GPHADVTAAGLR------------------------------------------------
-14==            ASTS-TTQEPQ-------------------------------------------------
-15==            ISTS-TTQEQQ-------------------------------------------------
-16==            QSTT-TQEQ-Q-------------------------------------------------
-17==            QSTT-TQEQTQ-------------------------------------------------
-18==            SQSNSTVAQDK-------------------------------------------------
-19==            NQSSNTQTQEK-------------------------------------------------
-20==            QSQA-TASEAE-------------------------------------------------
-21==            QSQA-TASEAE-------------------------------------------------
-22==            QSQA-TTSEAE-------------------------------------------------
-23==            ASDTETTSEAD-------------------------------------------------
-24==            PSDTETTSEAE-------------------------------------------------
-25==            STTSGTTTVTDN------------------------------------------------
-26==            SEASATTTMEEK------------------------------------------------
-27==            EEEV-VASERG--GESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPPQGA
-28==            ETEI-PAGESSDAAPSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPPQG-
-29==            HEALKLAERPERP-----------------EFVLQNA-----------------------
-30==            HEALKLAERPERS-----------------EFVLQNS-----------------------
-31=p            HEALKLAERPERS-----------------EFVLQNS-----------------------
-32==            ------------------------------------------------------------
-33=p            ------------------------------------------------------------
-34==            ------------------------------------------------------------
-35=p            ------------------------------------------------------------
-36==            ------------------------------------------------------------
-                                                                            
-
-1==             --------------------------------------------PVSP-A---
-2==             -----------------------------------------------P-A---
-3==             --------------------------------------------QVSP-A---
-4=p             -----------------------------------------------P-A---
-5=p             -----------------------------------------------P-A---
-6==             -----------------------------------------------PEK---
-7==             --------------------------------------------QVGP-N---
-8=opsin,        -----------------------------------------------------
-9==             --------------------------------------------SVSP-A---
-10==            --------------------------------------------SVSP-A---
-11==            --------------------------------------------SVAP-A---
-12==            --------------------------------------------SVSP-A---
-13==            -------------------------------------------NKVMP-AHPV
-14==            --------------------------------------------QTTA-A---
-15==            --------------------------------------------QTTA-A---
-16==            --------------------------------------------QTTA-A---
-17==            --------------------------------------------QTSA-A---
-18==            -------------------------------------------------A---
-19==            -------------------------------------------------S---
-20==            ----------------------------------------------SK-A---
-21==            ----------------------------------------------SK-A---
-22==            ----------------------------------------------SK-A---
-23==            ----------------------------------------------SK-A---
-24==            ----------------------------------------------SK-D---
-25==            -------------------------------------------EK-SN-A---
-26==            -------------------------------------------PKIPE-A---
-27==            YPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQ-A---
-28==            YPP-QGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQ-A---
-29==            -------------------------------------------DYCRKKGHDS
-30==            -------------------------------------------DHCGKKGHDT
-31=p            -------------------------------------------DHCGKKGHDT
-32==            -----------------------------------------------------
-33=p            -----------------------------------------------------
-34==            -----------------------------------------------------
-35=p            -----------------------------------------------------
-36==            -------------------------------------------------A-PQ
-                                                                     
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_default.aln	Wed Mar 20 07:34:52 2024 +0000
@@ -0,0 +1,468 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+----------------------------------------MNG----------------T
+E--G--DNFYVP----FSNKTGLARSPYEYPQY-------YLAEPWK---------YSAL
+AAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSM
+N-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGNTHAIM
+GVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESYVVYMF
+VVHFLVPFVIIFFCYGRLLCTV----KEAAAAQQ--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-H
+QGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC--------GKNPL
+GDDE--SGASTSKTEVSSVS-TSPVSPA--------------------------------
+---------------------------------------------------------
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+----------------------------------------MNG----------------T
+E--G--PNFYVP----FSNITGVVRSPFEQPQY-------YLAEPWQ---------FSML
+AAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSL
+H-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGENHAIM
+GVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMF
+VVHFTIPMIVIFFCYGQLVFTV----KEAAAQQQ--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-H
+QGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC--------GKNPL
+GDDE--ASATASKTE------TSQVAPA--------------------------------
+---------------------------------------------------------
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+----------------------------------------MNG----------------T
+E--G--INFYVP----MSNKTGVVRSPFEYPQY-------YLAEPWK---------YRLV
+CCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAW
+N-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSATHAMM
+GIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESYVLYMF
+VIHFIIPVVVIFFSYGRLICKV----REAAAQQQ--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-N
+KGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC--------GKNPF
+GDEDVSSTVSQSKTEVSSVS-SSQVSPA--------------------------------
+---------------------------------------------------------
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+----------------------------------------MNG----------------T
+E--G--KNFYVP----MSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKIL
+ALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAI
+N-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSSHAFA
+GIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNNESYVIYMF
+VCHFILPVAVIFFTYGRLVCTV----KAAAAQQQ--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-N
+KGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC--------GKNPL
+GDDE-SSTVSTSKTEVSS------VSPA--------------------------------
+---------------------------------------------------------
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+----------------------------------------MNG----------------T
+E--G--NNFYVP----LSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKLL
+AVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAI
+N-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSTHASA
+GIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNNESYVLYMF
+ICHFILPVTIIFFTYGRLVCTV----KAAAAQQQ--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-N
+KGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC--------GKNPL
+GDEE-SSTVSTSKTEVSS------VSPA--------------------------------
+---------------------------------------------------------
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+----------------------------------------MKQ----------------V
+PEFH--EDFYIPIPLDINNLS--AYSPFLVPQD-------HLGNQGI---------FMAM
+SVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSFF
+N-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FTFKTPHAIA
+GCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNNESYVMFLF
+CFCFAVPFGTIVFCYGQLLITL----KLAAKAQA--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------DSASTQK------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVS-H
+RGE--EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVC--------GKN-I
+EEDE--ASTSSQVTQVSS------VAPEK-------------------------------
+---------------------------------------------------------
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+----------------------------------------MRK----------------M
+S--E--EEFYL-----FKNIS--SVGPWDGPQY-------HIAPVWA---------FYLQ
+AAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPVFVASC
+N-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FRFSSKHALT
+VVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRSESYTWFLF
+IFCFIVPLSLICFSYTQLLRAL----KAVAAQQQ--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESATTQK------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN-N
+RNH--GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVC--------GKA-M
+TDES--DTCSSQKTEVSTVS-STQVGPN--------------------------------
+---------------------------------------------------------
+>     8=opsin, greensensitive  human (fragment) S07060
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------DLAETVIA-STISIVNQV
+S-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLAIV
+GIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
+VTCCITPLSIIVLCYLQVWLAI----RAVAKQQK--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESESTQK------AEKEVTRMVVVMVLAFC-----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+----------------------------------------MAQQWSLQRLAGRHPQDSYE
+DSTQ--SSIFT-----YTNSNS-TRGPFEGPNY-------HIAPRWV---------YHLT
+SVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQV
+Y-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VRFDAKLAIV
+GIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
+VTCCITPLSIIVLCYLQVWLAI----RAVAKQQK--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESESTQK------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA-N
+PGY--PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCIL-QLF---------GKK-V
+DDGS--ELSSASKTEVSSV---SSVSPA--------------------------------
+---------------------------------------------------------
+>    10== Z68193   1 human Red Opsin <>[]
+----------------------------------------MAQQWSLQRLAGRHPQDSYE
+DSTQ--SSIFT-----YTNSNS-TRGPFEGPNY-------HIAPRWV---------YHLT
+SVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQV
+S-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLAIV
+GIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
+VTCCIIPLAIIMLCYLQVWLAI----RAVAKQQK--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESESTQK------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA-N
+PGY--AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCIL-QLF---------GKK-V
+DDGS--ELSSASKTEVSSV---SSVSPA--------------------------------
+---------------------------------------------------------
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+----------------------------------------MTEAWNVAVFAARRSRDD-D
+DTTR--GSVFT-----YTNTNN-TRGPFEGPNY-------HIAPRWV---------YNLV
+SFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQI
+F-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IKFDSKLAII
+GIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLM
+ITCCFLPLFIIIVCYLQVWMAI----RAVAAQQK--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESESTQK------AEREVSRMVVVMIVAFCICWGPYASFVSFAAA-N
+PGY--AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIM-QLF---------GKK-V
+DDGS--EASTTSRTEVSSVS-NSSVAPA--------------------------------
+---------------------------------------------------------
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+----------------------------------------MAA-WEAAFAARRRHEE--E
+DTTR--DSVFT-----YTNSNN-TRGPFEGPNY-------HIAPRWV---------YNLT
+SVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQI
+S-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IKFDGKLAVA
+GILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLM
+VTCCFFPLAIIILCYLQVWLAI----RAVAAQQK--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------ESESTQK------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA-N
+PGY--AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIL-QLF---------GKK-V
+DDGS--EVST-SRTEVSSVS-NSSVSPA--------------------------------
+---------------------------------------------------------
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+----------------------------------------MS-----------------S
+NSSQ--AP-----------PNG-TPGPFDGPQW------PYQAPQST---------YVGV
+AVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNNI
+N-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQFQRRHAVS
+GCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--NSYILSLF
+VTCFVLPLSLILFSYTNLLLTL----RAAAAQQK--------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------EADTTQR------AEREVTRMVIVMVMAFLLCWLPYSTFALVVAT-H
+KGI--IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLL-EMLCCGY----QPQR-T
+GKAS--PGTPGPHADVTAAGLRNKVMPAHPV-----------------------------
+---------------------------------------------------------
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+----------MESGNVSS------------SLFGNVST-ALRP----------------E
+ARLS--A----------ETRLLGWNVPPEELR--------HIPEHWLTYPEPPESMNYLL
+GTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIFIYNSF
+H-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTHGKAIA
+MIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIF
+FFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKK-------------------------
+--------------------------------------------------MN--------
+--VESL------------------------------------------------------
+----------RSNVDKNKET------AEIRIAKAAITICFLFFCSWTPYGVMSLIGAF-G
+DKT--LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL---------N
+EKAP--ESSAVASTSTTQEP--QQTTAA--------------------------------
+---------------------------------------------------------
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+----------MEYHNVSS------------VL-GNVSS-VLRP----------------D
+ARLS--A----------ESRLLGWNVPPDELR--------HIPEHWLIYPEPPESMNYLL
+GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIFIYNSF
+H-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTHGKAIA
+MIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIF
+FFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKK-------------------------
+--------------------------------------------------MN--------
+--VDSL------------------------------------------------------
+----------RSNVDKSKEA------AEIRIAKAAITICFLFFASWTPYGVMSLIGAF-G
+DKT--LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI---------S
+EKAP--ESRAAISTSTTQEQ--QQTTAA--------------------------------
+---------------------------------------------------------
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+----------ME------------------PL-CNASEPPLRP----------------E
+AR-S--SG---N----GDLQFLGWNVPPDQIQ--------YIPEHWLTQLEPPASMHYML
+GVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF--NSF
+H-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVI
+MNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIF
+FFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKK-------------------------
+--------------------------------------------------MN--------
+--VESL------------------------------------------------------
+----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-G
+DKS--LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV---------N
+EKSG--EISSAQST-TTQEQ--QQTTAA--------------------------------
+---------------------------------------------------------
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+----------MD------------------AL-CNASEPPLRP----------------E
+ARMS--SG---S----DELQFLGWNVPPDQIQ--------YIPEHWLTQLEPPASMHYML
+GVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIFIYNSF
+H-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVI
+MNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIF
+LFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKK-------------------------
+--------------------------------------------------MN--------
+--VESL------------------------------------------------------
+----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-G
+DKS--LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV---------N
+EKSG--EASSAQST-TTQEQ-TQQTSAA--------------------------------
+---------------------------------------------------------
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+--------------------------------MTNATGPQMAY----------------Y
+GAAS--MD-FGY----PEGVSIVDFVRPEIKP--------YVHQHWYNYPPVNPMWHYLL
+GVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNCF
+SGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PKLTTGKAVV
+FALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNTFSYNIFIF
+VFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKK-------------------------
+--------------------------------------------------MN--------
+--VSTL------------------------------------------------------
+----------RS-NEADAQR------AEIRIAKTALVNVSLWFICWTPYALISLKGVM-G
+DTS--GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HE-T
+ETKS--NDDSQSNSTVAQDK-A--------------------------------------
+---------------------------------------------------------
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+--------------------------------MANVTGPQMAF----------------Y
+GSGA--AT-FGY----PEGMTVADFVPDRVKH--------MVLDHWYNYPPVNPMWHYLL
+GVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNCF
+SGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PKLTQGKATF
+MCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNTITYNICIF
+IFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKK-------------------------
+--------------------------------------------------MN--------
+--VTNL------------------------------------------------------
+----------RS-NEAETQR------AEIRIAKTALVNVSLWFICWTPYAAITIQGLL-G
+NAE--GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HE-K
+DPND--VEENQSSNTQTQEK-S--------------------------------------
+---------------------------------------------------------
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+----------ME----SF------------AVAAAQLGPHFAP----------------L
+S-----------------NGSVVDKVTPDMAH--------LISPYWNQFPAMDPIWAKIL
+TAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
+F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
+KM---------------------------YVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
+IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
+--------------------------------------------------MN--------
+--VKSL------------------------------------------------------
+----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-K
+F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
+DDGK--SSDAQSQA-TASEA-ESKA-----------------------------------
+---------------------------------------------------------
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+----------ME----SF------------AVAAAQLGPHFAP----------------L
+S-----------------NGSVVDKVTPDMAH--------LISPYWNQFPAMDPIWAKIL
+TAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
+F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
+KIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
+IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
+--------------------------------------------------MN--------
+--VKSL------------------------------------------------------
+----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-K
+F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
+DDGK--SSDAQSQA-TASEA-ESKA-----------------------------------
+---------------------------------------------------------
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+----------MD----SF------------AAVATQLGPQFAA----------------P
+S-----------------NGSVVDKVTPDMAH--------LISPYWDQFPAMDPIWAKIL
+TAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
+F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
+KIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
+IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
+--------------------------------------------------MN--------
+--VKSL------------------------------------------------------
+----------RS-SEDADKS------AEGKLAKVALVTISLWFMAWTPYLVINCMGLF-K
+F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
+DDGK--SSEAQSQA-TTSEA-ESKA-----------------------------------
+---------------------------------------------------------
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+-----MERSHLP----ET------------PFDLAHSGPRFQA----------------Q
+SSG---------------NGSVLDNVLPDMAH--------LVNPYWSRFAPMDPMMSKIL
+GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFY
+Y-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIM
+KILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNPRSYLITYS
+LFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKK-------------------------
+--------------------------------------------------MN--------
+--VKSL------------------------------------------------------
+----------RS-SEDCDKS------AEGKLAKVALTTISLWFMAWTPYLVICYFGLF-K
+I-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GN-T
+DEPK--PDAPASDTETTSEA-DSKA-----------------------------------
+---------------------------------------------------------
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+-----MERSLLP----EP------------PLAMALLGPRFEA----------------Q
+TGG---------------NRSVLDNVLPDMAP--------LVNPHWSRFAPMDPTMSKIL
+GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFY
+Y-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIM
+KIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNPRSYLITYS
+LFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKK-------------------------
+--------------------------------------------------MN--------
+--VKSL------------------------------------------------------
+----------RS-SEDCDKS------AENKLAKVALTTISLWFMAWTPYLIICYFGLF-K
+I-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GT-T
+DEPK--PDAPPSDTETTSEA-ESKD-----------------------------------
+---------------------------------------------------------
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+--------------------------------MIAVSGPSYEA----------------F
+SYGG--QARF-------NNQTVVDKVPPDMLH--------LIDANWYQYPPLNPMWHGIL
+GFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINCY
+Y-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KPLSINGALI
+RIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLSASYLVCYG
+IWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKK-------------------------
+--------------------------------------------------MN--------
+--VASL------------------------------------------------------
+----------RS-SENQNTS------AECKLAKVALMTISLWFMAWTPYLVINFSGIF-N
+L-V--KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------A-A
+EPSS--DAVSTTSGTTTVTD-NEKSNA---------------------------------
+---------------------------------------------------------
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+----------------------------------MANQLSYSS----------------L
+GWPY--QP----------NASVVDTMPKEMLY--------MIHEHWYAFPPMNPLWYSIL
+GVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNCF
+A-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-APLTHKKATL
+LLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSSASYVVIYG
+LAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKK-------------------------
+--------------------------------------------------MN--------
+--VASL------------------------------------------------------
+----------RANADQQKQS------AECRLAKVAMMTVGLWFMAWTPYLIISWAGVF-S
+SGT--RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GS-G
+ESGS--DVKSEASATTTMEE-KPKIPEA--------------------------------
+---------------------------------------------------------
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+---------------------------------------MVES----------------T
+TLVN--QT-WWY------NPTVD------------------IHPHWAKFDPIPDAVYYSV
+GIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAF
+M-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFL
+MIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPSTRSFILCMY
+FCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKR-------------------------
+--------------------------------------------------LN--------
+--AKEL------------------------------------------------------
+----------R--KAQAGAS------AEMKLAKISMVIITQFMLSWSPYAIIALLAQF-G
+PAE--WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKE-C
+EDAN--DAEEEVVASER--G-GESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PP
+QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+----------------------------------------MGR----------------D
+LRDN--ET-WWY------NPSIV------------------VHPHWREFDQVPDAVYYSL
+GIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCF
+L-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFI
+MIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTTRSNILCMF
+ILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR-------------------------
+--------------------------------------------------LN--------
+--AKEL------------------------------------------------------
+----------R--KAQAGAN------AEMRLAKISIVIVSQFLLSWSPYAVVALLAQF-G
+PLE--WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKE-T
+EDDK--DAETEIPAGESSDA-APSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPP
+QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+---------MMDVNSSGRPDLYGHLRSFL-LPEVGRGLPDLSPDGGA------------D
+PVAGSWAPHLLS------EVTASPAPTWDAPPDNASGCGEQIN--------YGRVEKVVI
+GSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
+IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
+MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
+AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
+---------------------------------PGFPRV----EPDSVIALNG-------
+--IVKL----------------------QK---------EVEECAN--------------
+----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
+GTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR----NINR--
+------KLSAAGMHEALKLAERPERPEF------------VLQNADY-------------
+--------------------------------------------CRKKGHDS-----
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+------------------------------------------------------------
+------MPHLLS---GFLEVTASPAPTWDAPPDNVSGCGEQIN--------YGRVEKVVI
+GSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
+IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
+MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
+AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
+---------------------------------PGFPRV----QPESVISLNG-------
+--VVKL----------------------QK---------EVEECAN--------------
+----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
+GTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYR----NINR--
+------KLSAAGMHEALKLAERPERSEF------------VLQNSDH-------------
+--------------------------------------------CGKKGHDT-----
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+------------------------------------------------------------
+------MPHLLS---GFLEVTASPAPTWDAPPDNVSGCGEQIN--------YGRVEKVVI
+GSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
+IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
+MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
+AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
+---------------------------------PGFPRV----QPESVISLNG-------
+--VVKL----------------------QK---------EVEECAN--------------
+----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
+GTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR----NINR--
+------KLSAAGMHEALKLAERPERSEF------------VLQNSDH-------------
+--------------------------------------------CGKKGHDT-----
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+----------MDVLSP--------------------------------------------
+---------------GQGNNTTSPPAPFET-GGNTTGISDVT---------VSYQ--VIT
+SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV
+L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA
+LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST
+FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------
+--------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR--
+-------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG--
+PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C
+ESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RQ----
+------------------------------------------------------------
+---------------------------------------------------------
+>    33=p A35181 serotonin receptor class 1A - rat
+----------MDVFSF--------------------------------------------
+---------------GQGNNTTASQEPFGT-GGNVTSISDVT---------FSYQ--VIT
+SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV
+L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA
+LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST
+FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------
+--------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG--
+-------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG--
+SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C
+ESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RR----
+------------------------------------------------------------
+---------------------------------------------------------
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T
+SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT
+SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI
+S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL
+MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST
+VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY
+SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---
+-------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--
+-----------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V
+DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--
+------------------------------------------------------------
+---------------------------------------------------------
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T
+SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT
+SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI
+S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL
+MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST
+VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY
+SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---
+-------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--
+-----------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V
+DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--
+------------------------------------------------------------
+---------------------------------------------------------
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+-MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGWEPNWNV------------T
+VVPN--TTWW------------QASAPFDTPAALVRAAAK--------------------
+AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEV
+V-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRVGM
+MIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV----------GYQIFAT
+ASSFYVPVLIILILYWRIY-------QTARKRIR--------------------------
+-------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGIA
+AAVVAVIGRPLPTISETTTTGFTNVSS----NNTSP---EKQSCANGLEADPPTTGYGAV
+AAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-C
+DCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV----RRRR--
+------A---------------PQ------------------------------------
+---------------------------------------------------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_explicit_amino_blosum80.clustal.aln	Wed Mar 20 07:34:52 2024 +0000
@@ -0,0 +1,458 @@
+CLUSTAL format alignment by MAFFT FFT-NS-2 (v7.520)
+
+
+1==             ----------------------------------------MN------------------
+2==             ----------------------------------------MN------------------
+3==             ----------------------------------------MN------------------
+4=p             ----------------------------------------MN------------------
+5=p             ----------------------------------------MN------------------
+6==             ----------------------------------------MK------------------
+7==             ----------------------------------------MR------------------
+8=opsin,        ------------------------------------------------------------
+9==             ----------------------------------------MAQQWSLQRLAGRHPQDS--
+10==            ----------------------------------------MAQQWSLQRLAGRHPQDS--
+11==            ----------------------------------------MTEAWNVAVFAARRSRDD--
+12==            ----------------------------------------MA-AWEAAFAARRRHEE---
+13==            ----------------------------------------MS------------------
+14==            ----------MESGNVS-------------SSLFGNVSTALR------------------
+15==            ----------MEYHNVS-------------SVL-GNVSSVLR------------------
+16==            ----------ME-------------------PLCNASEPPLR------------------
+17==            ----------MD-------------------ALCNASEPPLR------------------
+18==            --------------------------------MTNATGPQMA------------------
+19==            --------------------------------MANVTGPQMA------------------
+20==            ----------ME---SF-------------AVAAAQLGPHFA------------------
+21==            ----------ME---SF-------------AVAAAQLGPHFA------------------
+22==            ----------MD---SF-------------AAVATQLGPQFA------------------
+23==            -----MERSHLP---ET-------------PFDLAHSGPRFQ------------------
+24==            -----MERSLLP---EP-------------PLAMALLGPRFE------------------
+25==            --------------------------------MIAVSGPSYE------------------
+26==            ----------------------------------MANQLSYS------------------
+27==            ---------------------------------------MVE------------------
+28==            ----------------------------------------MG------------------
+29==            ---------MMDVNSSGRPDLYGHLRSFL-LPEVGRGLPDLSPDGGADPVAG-SWAPHLL
+30==            -------------------------------------------------------MPHLL
+31=p            -------------------------------------------------------MPHLL
+32==            ----------MDVLSP--------------------------------------------
+33=p            ----------MDVFSF--------------------------------------------
+34==            MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYG---L
+35=p            MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYG---L
+36==            -MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGWEPNWNVTVVPNTTW-----
+                                                                            
+
+1==             -----GTE--GDN-FYVP----FSNKTGLARSPYEYPQY-YLAEPWK-----------YS
+2==             -----GTE--GPN-FYVP----FSNITGVVRSPFEQPQY-YLAEPWQ-----------FS
+3==             -----GTE--GIN-FYVP----MSNKTGVVRSPFEYPQY-YLAEPWK-----------YR
+4=p             -----GTE--GKN-FYVP----MSNRTGLVRSPFEYPQY-YLAEPWQ-----------FK
+5=p             -----GTE--GNN-FYVP----LSNRTGLVRSPFEYPQY-YLAEPWQ-----------FK
+6==             -----QVPEFHED-FYIPIPLDINNLSAY--SPFLVPQD-HLGNQGI-----------FM
+7==             -----KMS--EEE-FYL-----FKNISSV--GPWDGPQY-HIAPVWA-----------FY
+8=opsin,        ------------------------------------------------------------
+9==             ----YEDSTQSSI-FT------YTNSNST-RGPFEGPNY-HIAPRWV-----------YH
+10==            ----YEDSTQSSI-FT------YTNSNST-RGPFEGPNY-HIAPRWV-----------YH
+11==            -----DDTTRGSV-FT------YTNTNNT-RGPFEGPNY-HIAPRWV-----------YN
+12==            -----EDTTRDSV-FT------YTNSNNT-RGPFEGPNY-HIAPRWV-----------YN
+13==            -----SNSSQAP-------------PNGT-PGPFDGPQWPYQAPQST-----------YV
+14==            -----PEARLSA-----------ETRLLGWNVPPEELR--HIPEHWLT--YPEPPESMNY
+15==            -----PDARLSA-----------ESRLLGWNVPPDELR--HIPEHWLI--YPEPPESMNY
+16==            -----PEAR-SSG---N-----GDLQFLGWNVPPDQIQ--YIPEHWLT--QLEPPASMHY
+17==            -----PEARMSSG---S-----DELQFLGWNVPPDQIQ--YIPEHWLT--QLEPPASMHY
+18==            -----YYGAASMD-FGY-----PEGVSIVDFVRPEIKP--YVHQHWYN--YPPVNPMWHY
+19==            -----FYGSGAAT-FGY-----PEGMTVADFVPDRVKH--MVLDHWYN--YPPVNPMWHY
+20==            -----PLS----------------NGSVVDKVTPDMAH--LISPYWNQ--FPAMDPIWAK
+21==            -----PLS----------------NGSVVDKVTPDMAH--LISPYWNQ--FPAMDPIWAK
+22==            -----APS----------------NGSVVDKVTPDMAH--LISPYWDQ--FPAMDPIWAK
+23==            -----AQSSG--------------NGSVLDNVLPDMAH--LVNPYWSR--FAPMDPMMSK
+24==            -----AQTGG--------------NRSVLDNVLPDMAP--LVNPHWSR--FAPMDPTMSK
+25==            -----AFSYGGQARF--------NNQTVVDKVPPDMLH--LIDANWYQ--YPPLNPMWHG
+26==            -----SLGWPYQP-----------NASVVDTMPKEMLY--MIHEHWYA--FPPMNPLWYS
+27==            -----STTLVNQT-WWY-------NPTVD------------IHPHWAK--FDPIPDAVYY
+28==            -----RDLRDNET-WWY-------NPSIV------------VHPHWRE--FDQVPDAVYY
+29==            S---EVTASPAPT-WDAP----PDNASGCGEQIN----------------YGRVE---KV
+30==            SGFLEVTASPAPT-WDAP----PDNVSGCGEQIN----------------YGRVE---KV
+31=p            SGFLEVTASPAPT-WDAP----PDNVSGCGEQIN----------------YGRVE---KV
+32==            -GQGNNTTSPPAP-FET-----GGNTTGISDVT-----------------VSYQ-----V
+33=p            -GQGNNTTASQEP-FGT-----GGNVTSISDVT-----------------FSYQ-----V
+34==            TGQFINGSHSSRS-RDNA----SANDTSATNMTDD--------RYWSLTVYSHEH---LV
+35=p            TGQFINGSHSSRS-RDNA----SANDTSATNMTDD--------RYWSLTVYSHEH---LV
+36==            -------WQASAP-FDTP----AALVRAAAK-----------------------------
+                                                                            
+
+1==             ALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYT
+2==             MLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYT
+3==             LVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYT
+4=p             ILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYT
+5=p             LLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYT
+6==             AMSVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYS
+7==             LQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPVFVA
+8=opsin,        --------------------------------------------DLAETVIA-STISIVN
+9==             LTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVN
+10==            LTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVN
+11==            LVSFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFN
+12==            LTSVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVIN
+13==            GVAVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSN
+14==            LLGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIFIYN
+15==            LLGTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIFIYN
+16==            MLGVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF--N
+17==            MLGVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIFIYN
+18==            LLGVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYN
+19==            LLGVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYN
+20==            ILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGIN
+21==            ILTAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGIN
+22==            ILTAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGIN
+23==            ILGLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIIN
+24==            ILGLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIIN
+25==            ILGFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVIN
+26==            ILGVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSN
+27==            SVGIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTIS
+28==            SLGIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTIS
+29==            VIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVT
+30==            VIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVT
+31=p            VIGSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVT
+32==            ITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALY
+33=p            ITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALY
+34==            LTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVS
+35=p            LTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVS
+36==            --AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVY
+                                                            .               
+
+1==             SMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGNTHA
+2==             SLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGENHA
+3==             AWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSATHA
+4=p             AIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSSHA
+5=p             AIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSTHA
+6==             FFN-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FTFKTPHA
+7==             SCN-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FRFSSKHA
+8=opsin,        QVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLA
+9==             QVY-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VRFDAKLA
+10==            QVS-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLA
+11==            QIF-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IKFDSKLA
+12==            QIS-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IKFDGKLA
+13==            NIN-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQFQRRHA
+14==            SFH-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTHGKA
+15==            SFH-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTHGKA
+16==            SFH-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKA
+17==            SFH-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKA
+18==            CFSGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PKLTTGKA
+19==            CFSGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PKLTQGKA
+20==            LYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLA
+21==            LYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLA
+22==            LYF-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLA
+23==            FYY-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTS
+24==            FYY-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTS
+25==            CYY-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KPLSINGA
+26==            CFA-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-APLTHKKA
+27==            AFM-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRA
+28==            CFL-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRA
+29==            DLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
+30==            DLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
+31=p            DLIGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCM
+32==            QVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRA
+33=p            QVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRA
+34==            EIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRI
+35=p            EIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRI
+36==            EVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRV
+                      :   :    * :                  :  :*:  :   :           
+
+1==             IMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESYVVY
+2==             IMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESFVIY
+3==             MMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESYVLY
+4=p             FAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNNESYVIY
+5=p             SAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNNESYVLY
+6==             IAGCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNNESYVMF
+7==             LTVVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRSESYTWF
+8=opsin,        IVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIV
+9==             IVGIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIV
+10==            IVGIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIV
+11==            IIGIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGCQSFMLT
+12==            VAGILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGVQSYMVV
+13==            VSGCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--NSYILS
+14==            IAMIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFVAC
+15==            IAMIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFVAC
+16==            VIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFVGT
+17==            VIMNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFVGT
+18==            VVFALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNTFSYNIF
+19==            TFMCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNTITYNIC
+20==            LGKM---------------------------YVPEGNLTSCGIDYLE--RDWNPRSYLIF
+21==            LGKIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYLIF
+22==            LGKIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYLIF
+23==            IMKILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNPRSYLIT
+24==            IMKIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNPRSYLIT
+25==            LIRIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLSASYLVC
+26==            TLLLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSSASYVVI
+27==            FLMIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPSTRSFILC
+28==            FIMIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTTRSNILC
+29==            AKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIY
+30==            AKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIY
+31=p            AKMILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIY
+32==            AALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIY
+33=p            AALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIY
+34==            LLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIF
+35=p            LLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIF
+36==            GMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV----------GYQIF
+                                                           :                
+
+1==             MFVVHFLVPFVIIFFCYGRLLCTV----KE------------------------------
+2==             MFVVHFTIPMIVIFFCYGQLVFTV----KE------------------------------
+3==             MFVIHFIIPVVVIFFSYGRLICKV----RE------------------------------
+4=p             MFVCHFILPVAVIFFTYGRLVCTV----KA------------------------------
+5=p             MFICHFILPVTIIFFTYGRLVCTV----KA------------------------------
+6==             LFCFCFAVPFGTIVFCYGQLLITL----KL------------------------------
+7==             LFIFCFIVPLSLICFSYTQLLRAL----KA------------------------------
+8=opsin,        LMVTCCITPLSIIVLCYLQVWLAI----RA------------------------------
+9==             LMVTCCITPLSIIVLCYLQVWLAI----RA------------------------------
+10==            LMVTCCIIPLAIIMLCYLQVWLAI----RA------------------------------
+11==            LMITCCFLPLFIIIVCYLQVWMAI----RA------------------------------
+12==            LMVTCCFFPLAIIILCYLQVWLAI----RA------------------------------
+13==            LFVTCFVLPLSLILFSYTNLLLTL----RA------------------------------
+14==            IFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------------
+15==            IFFFSFVCPTTMITYYYSQIVGHVFSHEKA------------------------------
+16==            IFFFSFVCPTLMILYYYSQIVGHVFSHEKA------------------------------
+17==            IFLFSFVVPTLMILYYYSQIVGHVFNHEKA------------------------------
+18==            IFVFDYFLPAAIIVFSYVFIVKAIFAHEAA------------------------------
+19==            IFIFDFFLPASVIVFSYVFIVKAIFAHEAA------------------------------
+20==            YSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------------
+21==            YSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------------
+22==            YSIFVYYIPLFLICYSYWFIIAAVSAHEKA------------------------------
+23==            YSLFVYYTPLFLICYSYWFIIAAVAAHEKA------------------------------
+24==            YSLFVYYTPLFMICYSYWFIIATVAAHEKA------------------------------
+25==            YGIWVYFVPLFLIIYSYWFIIQAVAAHEKN------------------------------
+26==            YGLAVYFLPLITMIYCYFFIVHAVAEHEKQ------------------------------
+27==            MYFCGFMLPIIIIAFCYFNIVMSVSNHEKE------------------------------
+28==            MFILGFFGPILIIFFCYFNIVMSVSNHEKE------------------------------
+29==            STAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF-----------------PGF-------
+30==            STAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF-----------------PGF-------
+31=p            STAVAFYIPMSVMLFMYYQIYKAARKSAAKHKF-----------------PGF-------
+32==            STFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------------
+33=p            STFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------------
+34==            STVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVVSD
+35=p            STVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTEYSVVSD
+36==            ATASSFYVPVLIILILYWRIYQTARKRIR-------------------------------
+                        *   :   *  :                                        
+
+1==             --------------------------AAAAQQ----------------------------
+2==             --------------------------AAAQQQ----------------------------
+3==             --------------------------AAAQQQ----------------------------
+4=p             --------------------------AAAQQQ----------------------------
+5=p             --------------------------AAAQQQ----------------------------
+6==             --------------------------AAKAQA----------------------------
+7==             --------------------------VAAQQQ----------------------------
+8=opsin,        --------------------------VAKQQK----------------------------
+9==             --------------------------VAKQQK----------------------------
+10==            --------------------------VAKQQK----------------------------
+11==            --------------------------VAAQQK----------------------------
+12==            --------------------------VAAQQK----------------------------
+13==            --------------------------AAAQQK----------------------------
+14==            --------------------------LRDQAKKM----------------------NVES
+15==            --------------------------LRDQAKKM----------------------NVDS
+16==            --------------------------LREQAKKM----------------------NVES
+17==            --------------------------LREQAKKM----------------------NVES
+18==            --------------------------MRAQAKKM----------------------NVST
+19==            --------------------------MRAQAKKM----------------------NVTN
+20==            --------------------------MREQAKKM----------------------NVKS
+21==            --------------------------MREQAKKM----------------------NVKS
+22==            --------------------------MREQAKKM----------------------NVKS
+23==            --------------------------MREQAKKM----------------------NVKS
+24==            --------------------------MRDQAKKM----------------------NVKS
+25==            --------------------------MREQAKKM----------------------NVAS
+26==            --------------------------LREQAKKM----------------------NVAS
+27==            --------------------------MAAMAKRL----------------------NAKE
+28==            --------------------------MAAMAKRL----------------------NAKE
+29==            --------------------------PRVEPD------------------------SVIA
+30==            --------------------------PRVQPE------------------------SVIS
+31=p            --------------------------PRVQPE------------------------SVIS
+32==            ---------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR-------
+33=p            ---------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG-------
+34==            CNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--------
+35=p            CNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--------
+36==            --------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGIAAAVVA
+                                                                            
+
+1==             ------------------------------------------------------------
+2==             ------------------------------------------------------------
+3==             ------------------------------------------------------------
+4=p             ------------------------------------------------------------
+5=p             ------------------------------------------------------------
+6==             ------------------------------------------------------------
+7==             ------------------------------------------------------------
+8=opsin,        ------------------------------------------------------------
+9==             ------------------------------------------------------------
+10==            ------------------------------------------------------------
+11==            ------------------------------------------------------------
+12==            ------------------------------------------------------------
+13==            ------------------------------------------------------------
+14==            L-----------------------------------------------------------
+15==            L-----------------------------------------------------------
+16==            L-----------------------------------------------------------
+17==            L-----------------------------------------------------------
+18==            L-----------------------------------------------------------
+19==            L-----------------------------------------------------------
+20==            L-----------------------------------------------------------
+21==            L-----------------------------------------------------------
+22==            L-----------------------------------------------------------
+23==            L-----------------------------------------------------------
+24==            L-----------------------------------------------------------
+25==            L-----------------------------------------------------------
+26==            L-----------------------------------------------------------
+27==            L-----------------------------------------------------------
+28==            L-----------------------------------------------------------
+29==            L-----------------NGIVKLQ--------KEVEECAN------------------L
+30==            L-----------------NGVVKLQ--------KEVEECAN------------------L
+31=p            L-----------------NGVVKLQ--------KEVEECAN------------------L
+32==            --NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCA--
+33=p            --DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESGSNSYA--
+34==            --SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-------
+35=p            --SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-------
+36==            VIGRPLPTISETTTTGFTNVSS----NNTS---PEKQSCANGLEADPPTTGYGAVAAAYY
+                                                                            
+
+1==             --------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-HQGS--
+2==             --------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-HQGS--
+3==             --------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-NKGA--
+4=p             --------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-NKGA--
+5=p             --------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-NKGA--
+6==             --------DSASTQK------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVS-HRGE--
+7==             --------ESATTQK------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN-NRNH--
+8=opsin,        --------ESESTQK------AEKEVTRMVVVMVLAFC----------------------
+9==             --------ESESTQK------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA-NPGY--
+10==            --------ESESTQK------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA-NPGY--
+11==            --------ESESTQK------AEREVSRMVVVMIVAFCICWGPYASFVSFAAA-NPGY--
+12==            --------ESESTQK------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA-NPGY--
+13==            --------EADTTQR------AEREVTRMVIVMVMAFLLCWLPYSTFALVVAT-HKGI--
+14==            -----RSNVDKNKET------AEIRIAKAAITICFLFFCSWTPYGVMSLIGAF-GDKT--
+15==            -----RSNVDKSKEA------AEIRIAKAAITICFLFFASWTPYGVMSLIGAF-GDKT--
+16==            -----RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-GDKS--
+17==            -----RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-GDKS--
+18==            -----RS-NEADAQR------AEIRIAKTALVNVSLWFICWTPYALISLKGVM-GDTS--
+19==            -----RS-NEAETQR------AEIRIAKTALVNVSLWFICWTPYAAITIQGLL-GNAE--
+20==            -----RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-KF-E--
+21==            -----RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-KF-E--
+22==            -----RS-SEDADKS------AEGKLAKVALVTISLWFMAWTPYLVINCMGLF-KF-E--
+23==            -----RS-SEDCDKS------AEGKLAKVALTTISLWFMAWTPYLVICYFGLF-KI-D--
+24==            -----RS-SEDCDKS------AENKLAKVALTTISLWFMAWTPYLIICYFGLF-KI-D--
+25==            -----RS-SENQNTS------AECKLAKVALMTISLWFMAWTPYLVINFSGIF-NL-V--
+26==            -----RANADQQKQS------AECRLAKVAMMTVGLWFMAWTPYLIISWAGVF-SSGT--
+27==            -----R--KAQAGAS------AEMKLAKISMVIITQFMLSWSPYAIIALLAQF-GPAE--
+28==            -----R--KAQAGAN------AEMRLAKISIVIVSQFLLSWSPYAVVALLAQF-GPLE--
+29==            SRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCS
+30==            SRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCS
+31=p            SRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCS
+32==            PASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CESSC-
+33=p            PACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-CESSC-
+34==            ------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-VDPE--
+35=p            ------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-VDPE--
+36==            PSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-CDCE--
+                                      * .           :                       
+
+1==             DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC--------GKNPLGDDE-
+2==             NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC--------GKNPLGDDE-
+3==             DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC--------GKNPFGDEDV
+4=p             DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC--------GKNPLGDDE-
+5=p             AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC--------GKNPLGDEE-
+6==             EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMMKMV-C--------GKN-IEEDE-
+7==             GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIMKMV-C--------GKA-MTDES-
+8=opsin,        ------------------------------------------------------------
+9==             PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLF----------GKK-VDDGS-
+10==            AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLF----------GKK-VDDGS-
+11==            AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLF----------GKK-VDDGS-
+12==            AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCILQLF----------GKK-VDDGS-
+13==            IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLLEMLCCG-----YQPQR-TGKAS-
+14==            LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL---------NEKAP-
+15==            LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI---------SEKAP-
+16==            LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV---------NEKSG-
+17==            LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV---------NEKSG-
+18==            GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HE-TETKS-
+19==            GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HE-KDPND-
+20==            GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-VDDGK-
+21==            GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-VDDGK-
+22==            GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-VDDGK-
+23==            GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GN-TDEPK-
+24==            GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GT-TDEPK-
+25==            KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------A-AEPSS-
+26==            RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GS-GESGS-
+27==            WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKE-CEDAN-
+28==            WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKE-TEDDK-
+29==            CIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------------
+30==            CIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYR---------------
+31=p            CIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR---------------
+32==            HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------------
+33=p            HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------------
+34==            GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------------
+35=p            GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------------
+36==            -VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV---------------
+                                                                            
+
+1==             -SGASTSKTEVSSVS-TSPVSPA-------------------------------------
+2==             -ASATASKTE------TSQVAPA-------------------------------------
+3==             SSTVSQSKTEVSSVS-SSQVSPA-------------------------------------
+4=p             SSTVSTSKTEVSS------VSPA-------------------------------------
+5=p             SSTVSTSKTEVSS------VSPA-------------------------------------
+6==             -ASTSSQVTQVSS------VAPEK------------------------------------
+7==             -DTCSSQKTEVSTVS-STQVGPN-------------------------------------
+8=opsin,        ------------------------------------------------------------
+9==             -ELSSASKTEVSSV---SSVSPA-------------------------------------
+10==            -ELSSASKTEVSSV---SSVSPA-------------------------------------
+11==            -EASTTSRTEVSSVS-NSSVAPA-------------------------------------
+12==            -EVST-SRTEVSSVS-NSSVSPA-------------------------------------
+13==            -PGTPGPHADVTAAGLRNKVMPAHPV----------------------------------
+14==            -ESSAVASTSTTQEP--QQTTAA-------------------------------------
+15==            -ESRAAISTSTTQEQ--QQTTAA-------------------------------------
+16==            -EISSAQST-TTQEQ--QQTTAA-------------------------------------
+17==            -EASSAQST-TTQEQ-TQQTSAA-------------------------------------
+18==            -NDDSQSNSTVAQDK-A-------------------------------------------
+19==            -VEENQSSNTQTQEK-S-------------------------------------------
+20==            -SSDAQSQA-TASEA-ESKA----------------------------------------
+21==            -SSDAQSQA-TASEA-ESKA----------------------------------------
+22==            -SSEAQSQA-TTSEA-ESKA----------------------------------------
+23==            -PDAPASDTETTSEA-DSKA----------------------------------------
+24==            -PDAPPSDTETTSEA-ESKD----------------------------------------
+25==            -DAVSTTSGTTTVTD-NEKSNA--------------------------------------
+26==            -DVKSEASATTTMEE-KPKIPEA-------------------------------------
+27==            -DAEEEVVASER--G-GESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PPQGYPP
+28==            -DAETEIPAGESSDA-APSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPPQGYPP
+29==            -NINRKLSAAGMHEALKLAERPERPEFVL--------QNADY------------------
+30==            -NINRKLSAAGMHEALKLAERPERSEFVL--------QNSDH------------------
+31=p            -NINRKLSAAGMHEALKLAERPERSEFVL--------QNSDH------------------
+32==            -RQ---------------------------------------------------------
+33=p            -RR---------------------------------------------------------
+34==            -RGHR-------------------------------------------------------
+35=p            -RGHR-------------------------------------------------------
+36==            -RRRRA---------------PQ-------------------------------------
+                                                                            
+
+1==             ----------------------------------------------------
+2==             ----------------------------------------------------
+3==             ----------------------------------------------------
+4=p             ----------------------------------------------------
+5=p             ----------------------------------------------------
+6==             ----------------------------------------------------
+7==             ----------------------------------------------------
+8=opsin,        ----------------------------------------------------
+9==             ----------------------------------------------------
+10==            ----------------------------------------------------
+11==            ----------------------------------------------------
+12==            ----------------------------------------------------
+13==            ----------------------------------------------------
+14==            ----------------------------------------------------
+15==            ----------------------------------------------------
+16==            ----------------------------------------------------
+17==            ----------------------------------------------------
+18==            ----------------------------------------------------
+19==            ----------------------------------------------------
+20==            ----------------------------------------------------
+21==            ----------------------------------------------------
+22==            ----------------------------------------------------
+23==            ----------------------------------------------------
+24==            ----------------------------------------------------
+25==            ----------------------------------------------------
+26==            ----------------------------------------------------
+27==            QGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+28==            QGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
+29==            ---------------------------------------CRKKGHDS-----
+30==            ---------------------------------------CGKKGHDT-----
+31=p            ---------------------------------------CGKKGHDT-----
+32==            ----------------------------------------------------
+33=p            ----------------------------------------------------
+34==            ----------------------------------------------------
+35=p            ----------------------------------------------------
+36==            ----------------------------------------------------
+                                                                    
--- a/test-data/mafft_fftns_result.aln	Tue Oct 31 15:48:53 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,468 +0,0 @@
->     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
-----------------------------------------MNG----------------T
-E--G--DNFYVP----FSNKTGLARSPYEYPQY-------YLAEPWK---------YSAL
-AAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSM
-N-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGNTHAIM
-GVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESYVVYMF
-VVHFLVPFVIIFFCYGRLLCTV----KEAAAAQQ--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-H
-QGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC--------GKNPL
-GDDE--SGASTSKTEVSSVS-TSPVSPA--------------------------------
----------------------------------------------------------
->     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
-----------------------------------------MNG----------------T
-E--G--PNFYVP----FSNITGVVRSPFEQPQY-------YLAEPWQ---------FSML
-AAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSL
-H-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGENHAIM
-GVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMF
-VVHFTIPMIVIFFCYGQLVFTV----KEAAAQQQ--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-H
-QGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC--------GKNPL
-GDDE--ASATASKTE------TSQVAPA--------------------------------
----------------------------------------------------------
->     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
-----------------------------------------MNG----------------T
-E--G--INFYVP----MSNKTGVVRSPFEYPQY-------YLAEPWK---------YRLV
-CCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAW
-N-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSATHAMM
-GIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESYVLYMF
-VIHFIIPVVVIFFSYGRLICKV----REAAAQQQ--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-N
-KGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC--------GKNPF
-GDEDVSSTVSQSKTEVSSVS-SSQVSPA--------------------------------
----------------------------------------------------------
->     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
-----------------------------------------MNG----------------T
-E--G--KNFYVP----MSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKIL
-ALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAI
-N-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSSHAFA
-GIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNNESYVIYMF
-VCHFILPVAVIFFTYGRLVCTV----KAAAAQQQ--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-N
-KGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC--------GKNPL
-GDDE-SSTVSTSKTEVSS------VSPA--------------------------------
----------------------------------------------------------
->     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
-----------------------------------------MNG----------------T
-E--G--NNFYVP----LSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKLL
-AVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAI
-N-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSTHASA
-GIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNNESYVLYMF
-ICHFILPVTIIFFTYGRLVCTV----KAAAAQQQ--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-N
-KGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC--------GKNPL
-GDEE-SSTVSTSKTEVSS------VSPA--------------------------------
----------------------------------------------------------
->     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
-----------------------------------------MKQ----------------V
-PEFH--EDFYIPIPLDINNLS--AYSPFLVPQD-------HLGNQGI---------FMAM
-SVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSFF
-N-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FTFKTPHAIA
-GCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNNESYVMFLF
-CFCFAVPFGTIVFCYGQLLITL----KLAAKAQA--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------DSASTQK------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVS-H
-RGE--EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVC--------GKN-I
-EEDE--ASTSSQVTQVSS------VAPEK-------------------------------
----------------------------------------------------------
->     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
-----------------------------------------MRK----------------M
-S--E--EEFYL-----FKNIS--SVGPWDGPQY-------HIAPVWA---------FYLQ
-AAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPVFVASC
-N-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FRFSSKHALT
-VVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRSESYTWFLF
-IFCFIVPLSLICFSYTQLLRAL----KAVAAQQQ--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESATTQK------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN-N
-RNH--GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVC--------GKA-M
-TDES--DTCSSQKTEVSTVS-STQVGPN--------------------------------
----------------------------------------------------------
->     8=opsin, greensensitive  human (fragment) S07060
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------DLAETVIA-STISIVNQV
-S-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLAIV
-GIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
-VTCCITPLSIIVLCYLQVWLAI----RAVAKQQK--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESESTQK------AEKEVTRMVVVMVLAFC-----------------
-------------------------------------------------------------
-------------------------------------------------------------
----------------------------------------------------------
->     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
-----------------------------------------MAQQWSLQRLAGRHPQDSYE
-DSTQ--SSIFT-----YTNSNS-TRGPFEGPNY-------HIAPRWV---------YHLT
-SVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQV
-Y-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VRFDAKLAIV
-GIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
-VTCCITPLSIIVLCYLQVWLAI----RAVAKQQK--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESESTQK------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA-N
-PGY--PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCIL-QLF---------GKK-V
-DDGS--ELSSASKTEVSSV---SSVSPA--------------------------------
----------------------------------------------------------
->    10== Z68193   1 human Red Opsin <>[]
-----------------------------------------MAQQWSLQRLAGRHPQDSYE
-DSTQ--SSIFT-----YTNSNS-TRGPFEGPNY-------HIAPRWV---------YHLT
-SVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQV
-S-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLAIV
-GIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
-VTCCIIPLAIIMLCYLQVWLAI----RAVAKQQK--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESESTQK------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA-N
-PGY--AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCIL-QLF---------GKK-V
-DDGS--ELSSASKTEVSSV---SSVSPA--------------------------------
----------------------------------------------------------
->    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
-----------------------------------------MTEAWNVAVFAARRSRDD-D
-DTTR--GSVFT-----YTNTNN-TRGPFEGPNY-------HIAPRWV---------YNLV
-SFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQI
-F-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IKFDSKLAII
-GIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLM
-ITCCFLPLFIIIVCYLQVWMAI----RAVAAQQK--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESESTQK------AEREVSRMVVVMIVAFCICWGPYASFVSFAAA-N
-PGY--AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIM-QLF---------GKK-V
-DDGS--EASTTSRTEVSSVS-NSSVAPA--------------------------------
----------------------------------------------------------
->    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
-----------------------------------------MAA-WEAAFAARRRHEE--E
-DTTR--DSVFT-----YTNSNN-TRGPFEGPNY-------HIAPRWV---------YNLT
-SVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQI
-S-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IKFDGKLAVA
-GILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLM
-VTCCFFPLAIIILCYLQVWLAI----RAVAAQQK--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------ESESTQK------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA-N
-PGY--AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIL-QLF---------GKK-V
-DDGS--EVST-SRTEVSSVS-NSSVSPA--------------------------------
----------------------------------------------------------
->    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
-----------------------------------------MS-----------------S
-NSSQ--AP-----------PNG-TPGPFDGPQW------PYQAPQST---------YVGV
-AVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNNI
-N-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQFQRRHAVS
-GCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--NSYILSLF
-VTCFVLPLSLILFSYTNLLLTL----RAAAAQQK--------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------EADTTQR------AEREVTRMVIVMVMAFLLCWLPYSTFALVVAT-H
-KGI--IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLL-EMLCCGY----QPQR-T
-GKAS--PGTPGPHADVTAAGLRNKVMPAHPV-----------------------------
----------------------------------------------------------
->    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
-----------MESGNVSS------------SLFGNVST-ALRP----------------E
-ARLS--A----------ETRLLGWNVPPEELR--------HIPEHWLTYPEPPESMNYLL
-GTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIFIYNSF
-H-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTHGKAIA
-MIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIF
-FFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKK-------------------------
---------------------------------------------------MN--------
---VESL------------------------------------------------------
-----------RSNVDKNKET------AEIRIAKAAITICFLFFCSWTPYGVMSLIGAF-G
-DKT--LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL---------N
-EKAP--ESSAVASTSTTQEP--QQTTAA--------------------------------
----------------------------------------------------------
->    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
-----------MEYHNVSS------------VL-GNVSS-VLRP----------------D
-ARLS--A----------ESRLLGWNVPPDELR--------HIPEHWLIYPEPPESMNYLL
-GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIFIYNSF
-H-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTHGKAIA
-MIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIF
-FFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKK-------------------------
---------------------------------------------------MN--------
---VDSL------------------------------------------------------
-----------RSNVDKSKEA------AEIRIAKAAITICFLFFASWTPYGVMSLIGAF-G
-DKT--LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI---------S
-EKAP--ESRAAISTSTTQEQ--QQTTAA--------------------------------
----------------------------------------------------------
->    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
-----------ME------------------PL-CNASEPPLRP----------------E
-AR-S--SG---N----GDLQFLGWNVPPDQIQ--------YIPEHWLTQLEPPASMHYML
-GVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF--NSF
-H-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVI
-MNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIF
-FFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKK-------------------------
---------------------------------------------------MN--------
---VESL------------------------------------------------------
-----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-G
-DKS--LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV---------N
-EKSG--EISSAQST-TTQEQ--QQTTAA--------------------------------
----------------------------------------------------------
->    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
-----------MD------------------AL-CNASEPPLRP----------------E
-ARMS--SG---S----DELQFLGWNVPPDQIQ--------YIPEHWLTQLEPPASMHYML
-GVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIFIYNSF
-H-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVI
-MNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIF
-LFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKK-------------------------
---------------------------------------------------MN--------
---VESL------------------------------------------------------
-----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-G
-DKS--LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV---------N
-EKSG--EASSAQST-TTQEQ-TQQTSAA--------------------------------
----------------------------------------------------------
->    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
---------------------------------MTNATGPQMAY----------------Y
-GAAS--MD-FGY----PEGVSIVDFVRPEIKP--------YVHQHWYNYPPVNPMWHYLL
-GVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNCF
-SGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PKLTTGKAVV
-FALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNTFSYNIFIF
-VFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKK-------------------------
---------------------------------------------------MN--------
---VSTL------------------------------------------------------
-----------RS-NEADAQR------AEIRIAKTALVNVSLWFICWTPYALISLKGVM-G
-DTS--GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HE-T
-ETKS--NDDSQSNSTVAQDK-A--------------------------------------
----------------------------------------------------------
->    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
---------------------------------MANVTGPQMAF----------------Y
-GSGA--AT-FGY----PEGMTVADFVPDRVKH--------MVLDHWYNYPPVNPMWHYLL
-GVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNCF
-SGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PKLTQGKATF
-MCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNTITYNICIF
-IFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKK-------------------------
---------------------------------------------------MN--------
---VTNL------------------------------------------------------
-----------RS-NEAETQR------AEIRIAKTALVNVSLWFICWTPYAAITIQGLL-G
-NAE--GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HE-K
-DPND--VEENQSSNTQTQEK-S--------------------------------------
----------------------------------------------------------
->    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
-----------ME----SF------------AVAAAQLGPHFAP----------------L
-S-----------------NGSVVDKVTPDMAH--------LISPYWNQFPAMDPIWAKIL
-TAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
-F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
-KM---------------------------YVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
-IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
---------------------------------------------------MN--------
---VKSL------------------------------------------------------
-----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-K
-F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
-DDGK--SSDAQSQA-TASEA-ESKA-----------------------------------
----------------------------------------------------------
->    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
-----------ME----SF------------AVAAAQLGPHFAP----------------L
-S-----------------NGSVVDKVTPDMAH--------LISPYWNQFPAMDPIWAKIL
-TAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
-F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
-KIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
-IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
---------------------------------------------------MN--------
---VKSL------------------------------------------------------
-----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-K
-F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
-DDGK--SSDAQSQA-TASEA-ESKA-----------------------------------
----------------------------------------------------------
->    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
-----------MD----SF------------AAVATQLGPQFAA----------------P
-S-----------------NGSVVDKVTPDMAH--------LISPYWDQFPAMDPIWAKIL
-TAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
-F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
-KIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
-IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
---------------------------------------------------MN--------
---VKSL------------------------------------------------------
-----------RS-SEDADKS------AEGKLAKVALVTISLWFMAWTPYLVINCMGLF-K
-F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
-DDGK--SSEAQSQA-TTSEA-ESKA-----------------------------------
----------------------------------------------------------
->    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
------MERSHLP----ET------------PFDLAHSGPRFQA----------------Q
-SSG---------------NGSVLDNVLPDMAH--------LVNPYWSRFAPMDPMMSKIL
-GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFY
-Y-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIM
-KILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNPRSYLITYS
-LFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKK-------------------------
---------------------------------------------------MN--------
---VKSL------------------------------------------------------
-----------RS-SEDCDKS------AEGKLAKVALTTISLWFMAWTPYLVICYFGLF-K
-I-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GN-T
-DEPK--PDAPASDTETTSEA-DSKA-----------------------------------
----------------------------------------------------------
->    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
------MERSLLP----EP------------PLAMALLGPRFEA----------------Q
-TGG---------------NRSVLDNVLPDMAP--------LVNPHWSRFAPMDPTMSKIL
-GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFY
-Y-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIM
-KIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNPRSYLITYS
-LFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKK-------------------------
---------------------------------------------------MN--------
---VKSL------------------------------------------------------
-----------RS-SEDCDKS------AENKLAKVALTTISLWFMAWTPYLIICYFGLF-K
-I-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GT-T
-DEPK--PDAPPSDTETTSEA-ESKD-----------------------------------
----------------------------------------------------------
->    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
---------------------------------MIAVSGPSYEA----------------F
-SYGG--QARF-------NNQTVVDKVPPDMLH--------LIDANWYQYPPLNPMWHGIL
-GFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINCY
-Y-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KPLSINGALI
-RIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLSASYLVCYG
-IWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKK-------------------------
---------------------------------------------------MN--------
---VASL------------------------------------------------------
-----------RS-SENQNTS------AECKLAKVALMTISLWFMAWTPYLVINFSGIF-N
-L-V--KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------A-A
-EPSS--DAVSTTSGTTTVTD-NEKSNA---------------------------------
----------------------------------------------------------
->    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
-----------------------------------MANQLSYSS----------------L
-GWPY--QP----------NASVVDTMPKEMLY--------MIHEHWYAFPPMNPLWYSIL
-GVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNCF
-A-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-APLTHKKATL
-LLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSSASYVVIYG
-LAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKK-------------------------
---------------------------------------------------MN--------
---VASL------------------------------------------------------
-----------RANADQQKQS------AECRLAKVAMMTVGLWFMAWTPYLIISWAGVF-S
-SGT--RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GS-G
-ESGS--DVKSEASATTTMEE-KPKIPEA--------------------------------
----------------------------------------------------------
->    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
----------------------------------------MVES----------------T
-TLVN--QT-WWY------NPTVD------------------IHPHWAKFDPIPDAVYYSV
-GIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAF
-M-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFL
-MIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPSTRSFILCMY
-FCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKR-------------------------
---------------------------------------------------LN--------
---AKEL------------------------------------------------------
-----------R--KAQAGAS------AEMKLAKISMVIITQFMLSWSPYAIIALLAQF-G
-PAE--WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKE-C
-EDAN--DAEEEVVASER--G-GESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PP
-QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
->    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
-----------------------------------------MGR----------------D
-LRDN--ET-WWY------NPSIV------------------VHPHWREFDQVPDAVYYSL
-GIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCF
-L-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFI
-MIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTTRSNILCMF
-ILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR-------------------------
---------------------------------------------------LN--------
---AKEL------------------------------------------------------
-----------R--KAQAGAN------AEMRLAKISIVIVSQFLLSWSPYAVVALLAQF-G
-PLE--WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKE-T
-EDDK--DAETEIPAGESSDA-APSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPP
-QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
->    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
----------MMDVNSSGRPDLYGHLRSFL-LPEVGRGLPDLSPDGGA------------D
-PVAGSWAPHLLS------EVTASPAPTWDAPPDNASGCGEQIN--------YGRVEKVVI
-GSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
-IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
-MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
-AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
----------------------------------PGFPRV----EPDSVIALNG-------
---IVKL----------------------QK---------EVEECAN--------------
-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
-GTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR----NINR--
-------KLSAAGMHEALKLAERPERPEF------------VLQNADY-------------
---------------------------------------------CRKKGHDS-----
->    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
-------------------------------------------------------------
-------MPHLLS---GFLEVTASPAPTWDAPPDNVSGCGEQIN--------YGRVEKVVI
-GSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
-IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
-MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
-AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
----------------------------------PGFPRV----QPESVISLNG-------
---VVKL----------------------QK---------EVEECAN--------------
-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
-GTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYR----NINR--
-------KLSAAGMHEALKLAERPERSEF------------VLQNSDH-------------
---------------------------------------------CGKKGHDT-----
->    31=p A47425 serotonin receptor 5HT-7 - rat
-------------------------------------------------------------
-------MPHLLS---GFLEVTASPAPTWDAPPDNVSGCGEQIN--------YGRVEKVVI
-GSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
-IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
-MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
-AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
----------------------------------PGFPRV----QPESVISLNG-------
---VVKL----------------------QK---------EVEECAN--------------
-----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
-GTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR----NINR--
-------KLSAAGMHEALKLAERPERSEF------------VLQNSDH-------------
---------------------------------------------CGKKGHDT-----
->    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
-----------MDVLSP--------------------------------------------
----------------GQGNNTTSPPAPFET-GGNTTGISDVT---------VSYQ--VIT
-SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV
-L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA
-LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST
-FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------
---------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR--
--------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG--
-PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C
-ESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RQ----
-------------------------------------------------------------
----------------------------------------------------------
->    33=p A35181 serotonin receptor class 1A - rat
-----------MDVFSF--------------------------------------------
----------------GQGNNTTASQEPFGT-GGNVTSISDVT---------FSYQ--VIT
-SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV
-L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA
-LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST
-FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------
---------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG--
--------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG--
-SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C
-ESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RR----
-------------------------------------------------------------
----------------------------------------------------------
->    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
-MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T
-SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT
-SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI
-S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL
-MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST
-VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY
-SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---
--------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--
------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V
-DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--
-------------------------------------------------------------
----------------------------------------------------------
->    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
-MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T
-SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT
-SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI
-S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL
-MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST
-VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY
-SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---
--------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--
------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V
-DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--
-------------------------------------------------------------
----------------------------------------------------------
->    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
--MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGWEPNWNV------------T
-VVPN--TTWW------------QASAPFDTPAALVRAAAK--------------------
-AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEV
-V-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRVGM
-MIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV----------GYQIFAT
-ASSFYVPVLIILILYWRIY-------QTARKRIR--------------------------
--------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGIA
-AAVVAVIGRPLPTISETTTTGFTNVSS----NNTSP---EKQSCANGLEADPPTTGYGAV
-AAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-C
-DCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV----RRRR--
-------A---------------PQ------------------------------------
----------------------------------------------------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mafft_kimura40.phylip.aln	Wed Mar 20 07:34:52 2024 +0000
@@ -0,0 +1,77 @@
+ 3 948
+MZ681498.1 atgcatgtat aagtataacc tgccagacag ggaaactgcg gacggctcat
+MZ681497.1 ---------- ---------- ---------- -----ctgcg gacggctcat
+ON855043.1 ---------- ---------- -ggccgtca- -----ctccg gggggacaac
+
+           tacaacagcc ttaatttact tgaccttgac aacctacttg gataactgcg
+           tacaacagcc ttaatttact tgaccttgac aacctacttg gataactgcg
+           acaaacgccc tgagggcttt actcgttggg gtgcaaactg ga--------
+
+           gtaattctgg agctaataca tgcaccaaag ctccgatccc tcgtggagag
+           gtaattctgg agctaataca tgcaccaaag ctccgatccc tcgtggagag
+           ---------- ---------- ---------- ---------- ---tcgagtg
+
+           gagcgcattt gttcgccaca aaaccaaacg ccccacaagg gcgttcagtg
+           gagcgcattt gttcgccaca aaaccaaacg ccccacaagg gcgttcagtg
+           gcgcacacat cccttccacg caa--agacc tgctgaagag gtcggaggcg
+
+           ttgactcaga ataact---- ---------- -------aag ctgatcgcac
+           ttgactcaga ataact---- ---------- -------aag ctgatcgcac
+           atgagtccga gcaaccccac aagcaaccag gttggggaag ctg--cacac
+
+           ggtctt---- ---------- ----gcaccg gcgacgtgtc tttcaagtgt
+           ggtctt---- ---------- ----gcaccg gcgacgtgtc tttcaagtgt
+           gatactggga tgcacgcccc cagggcacct aacggctgcc gctggcgtct
+
+           ctgccttatc aactttcgat ggtagtgtat ctgcctacca tggttgtgac
+           ctgccttatc aactttcgat ggtagtgtat ctgcctacca tggttgtgac
+           gtgcgtcgtt ga---gcagt tgttgcgcac ttgctt---- ttgtcggagc
+
+           gggtaacgga ggataagggt tcgactccgg agaaggggcc tgagaaatgg
+           gggtaacgga ggataagggt tcgactccgg agaaggggcc tgagaaatgg
+           tgtactcgga gcatgctggc atggacccac acaaaag--- ----------
+
+           ccactacgtc taaggatggc agcaggcgcg caaattaccc actctcaaca
+           ccactacgtc taaggatggc agcaggcgcg caaattaccc actctcaaca
+           ---------- --tgtgtggc agcggccaca ca------cc cctgtccatg
+
+           cgctgaggag gtagtgaaga gaaataacga gaccgttctc acatgaggcc
+           cgctgaggag gtagtgaaga gaaataacga gaccgttctc acatgaggcc
+           tcctacgga- ---------- -ccgtagcta gggcgtgct- ----------
+
+           ggtcatcgga atgggtacaa cttaaaccct ttaacgagta tctatgagag
+           ggtcatcgga atgggtacaa cttaaaccct ttaacgagta tctatgagag
+           ---------- ---------- ---------- ---------- ----------
+
+           ggcaagtctg gtgccagcag ccgcggtaat tccagctctc aaaatgcata
+           ggcaagtctg gtgccagcag ccgcggtaat tccagctctc aaaatgcata
+           ---------- ---------- -ctgggtttc ttcggctggc agtgttgcta
+
+           gaattattgc tgcggttaaa aagctcgtag ttggatctgt gctggccgcc
+           gaattattgc tgcggttaaa aagctcgtag ttggatctgt gctggccgcc
+           cgtccgtggc tgtgatgaga cgacgcg--- ---------- ----------
+
+           cggtctgctc gctgagcacg cactggtgcg gtcggctttc ctgcccggta
+           cggtctgctc gctgagcacg cactggtgcg gtcggctttc ctgcccggta
+           ---------- -----gtagg gccttgtgcg atgcgcct-- ----------
+
+           cctccccggc gttggccttc accggtcggc gtcggtggcc gggcgagttt
+           cctccccggc gttggccttc accggtcggc gtcggtggcc gggcgagttt
+           --------gc acttggctta a--------- ------gact tgatgagctc
+
+           actttgaaca aatcagag-- -----tgctt caaacaggcg tttcgcttga
+           actttgaaca aatcagag-- -----tgctt caaacaggcg tttcgcttga
+           actgcgaaga gccgccagca accttttttt catatacatt ttttacaggc
+
+           atgttcgtgc atggaataat agaagaggat ttcggtccga ttttgttggt
+           atgttcgtgc atggaataat agaagaggat ttcggtccga ttttgttggt
+           acacttgtgt gctgatgaac aaaa------ ---------- ----------
+
+           tttgctgacc gagataatgg ttaacagaga caaacggggc cattcgtatt
+           tttgctgacc gagataatgg ttaacagaga caaacggggc cattcgtatt
+           ---------- ---------- ---------- ---------- -------att
+
+           gctacgtgag aggtg----- ---------- ---------- --------
+           gctacgtgag aggtgaaatt cttggaccgt agcaagacgg actacagc
+           ctagccttat cggtggatca ctcggctcgt aggtcgatg- --------
+
--- a/test-data/mafft_nwns_result.aln	Tue Oct 31 15:48:53 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,458 +0,0 @@
-CLUSTAL format alignment by MAFFT NW-NS-2 (v7.455)
-
-
-1==             ----------------------------------------MNG----------------T
-2==             ----------------------------------------MNG----------------T
-3==             ----------------------------------------MNG----------------T
-4=p             ----------------------------------------MNG----------------T
-5=p             ----------------------------------------MNG----------------T
-6==             ----------------------------------------MKQ----------------V
-7==             ----------------------------------------MRK----------------M
-8=opsin,        ------------------------------------------------------------
-9==             ----------------------------------------MAQQWSLQRLAGRHPQDSYE
-10==            ----------------------------------------MAQQWSLQRLAGRHPQDSYE
-11==            ----------------------------------------MTEAWNVAVFAARRSRDD-D
-12==            ----------------------------------------MAA-WEAAFAARRRHEE--E
-13==            ----------------------------------------MS-----------------S
-14==            ----------MESGNVSS------------SLFGNVST-ALRP----------------E
-15==            ----------MEYHNVSS------------VL-GNVSS-VLRP----------------D
-16==            ----------ME------------------PL-CNASEPPLRP----------------E
-17==            ----------MD------------------AL-CNASEPPLRP----------------E
-18==            --------------------------------MTNATGPQMAY----------------Y
-19==            --------------------------------MANVTGPQMAF----------------Y
-20==            ----------ME----SF------------AVAAAQLGPHFAP----------------L
-21==            ----------ME----SF------------AVAAAQLGPHFAP----------------L
-22==            ----------MD----SF------------AAVATQLGPQFAA----------------P
-23==            -----MERSHLP----ET------------PFDLAHSGPRFQA----------------Q
-24==            -----MERSLLP----EP------------PLAMALLGPRFEA----------------Q
-25==            --------------------------------MIAVSGPSYEA----------------F
-26==            ----------------------------------MANQLSYSS----------------L
-27==            ---------------------------------------MVES----------------T
-28==            ----------------------------------------MGR----------------D
-29==            ---------MMDVNSSGRPDLYGHLRSFL-LPEVGRGLPDLSPDGGA------------D
-30==            ------------------------------------------------------------
-31=p            ------------------------------------------------------------
-32==            ----------MDVLSP--------------------------------------------
-33=p            ----------MDVFSF--------------------------------------------
-34==            MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T
-35=p            MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGLSPTGLV------------T
-36==            -MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGWEPNWNV------------T
-                                                                            
-
-1==             E--G--DNFYVP----FSNKTGLARSPYEYPQY-------YLAEPWK---------YSAL
-2==             E--G--PNFYVP----FSNITGVVRSPFEQPQY-------YLAEPWQ---------FSML
-3==             E--G--INFYVP----MSNKTGVVRSPFEYPQY-------YLAEPWK---------YRLV
-4=p             E--G--KNFYVP----MSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKIL
-5=p             E--G--NNFYVP----LSNRTGLVRSPFEYPQY-------YLAEPWQ---------FKLL
-6==             PEFH--EDFYIPIPLDINNLS--AYSPFLVPQD-------HLGNQGI---------FMAM
-7==             S--E--EEFYL-----FKNIS--SVGPWDGPQY-------HIAPVWA---------FYLQ
-8=opsin,        ------------------------------------------------------------
-9==             DSTQ--SSIFT-----YTNSNS-TRGPFEGPNY-------HIAPRWV---------YHLT
-10==            DSTQ--SSIFT-----YTNSNS-TRGPFEGPNY-------HIAPRWV---------YHLT
-11==            DTTR--GSVFT-----YTNTNN-TRGPFEGPNY-------HIAPRWV---------YNLV
-12==            DTTR--DSVFT-----YTNSNN-TRGPFEGPNY-------HIAPRWV---------YNLT
-13==            NSSQ--AP-----------PNG-TPGPFDGPQW------PYQAPQST---------YVGV
-14==            ARLS--A----------ETRLLGWNVPPEELR--------HIPEHWLTYPEPPESMNYLL
-15==            ARLS--A----------ESRLLGWNVPPDELR--------HIPEHWLIYPEPPESMNYLL
-16==            AR-S--SG---N----GDLQFLGWNVPPDQIQ--------YIPEHWLTQLEPPASMHYML
-17==            ARMS--SG---S----DELQFLGWNVPPDQIQ--------YIPEHWLTQLEPPASMHYML
-18==            GAAS--MD-FGY----PEGVSIVDFVRPEIKP--------YVHQHWYNYPPVNPMWHYLL
-19==            GSGA--AT-FGY----PEGMTVADFVPDRVKH--------MVLDHWYNYPPVNPMWHYLL
-20==            S-----------------NGSVVDKVTPDMAH--------LISPYWNQFPAMDPIWAKIL
-21==            S-----------------NGSVVDKVTPDMAH--------LISPYWNQFPAMDPIWAKIL
-22==            S-----------------NGSVVDKVTPDMAH--------LISPYWDQFPAMDPIWAKIL
-23==            SSG---------------NGSVLDNVLPDMAH--------LVNPYWSRFAPMDPMMSKIL
-24==            TGG---------------NRSVLDNVLPDMAP--------LVNPHWSRFAPMDPTMSKIL
-25==            SYGG--QARF-------NNQTVVDKVPPDMLH--------LIDANWYQYPPLNPMWHGIL
-26==            GWPY--QP----------NASVVDTMPKEMLY--------MIHEHWYAFPPMNPLWYSIL
-27==            TLVN--QT-WWY------NPTVD------------------IHPHWAKFDPIPDAVYYSV
-28==            LRDN--ET-WWY------NPSIV------------------VHPHWREFDQVPDAVYYSL
-29==            PVAGSWAPHLLS------EVTASPAPTWDAPPDNASGCGEQIN--------YGRVEKVVI
-30==            ------MPHLLS---GFLEVTASPAPTWDAPPDNVSGCGEQIN--------YGRVEKVVI
-31=p            ------MPHLLS---GFLEVTASPAPTWDAPPDNVSGCGEQIN--------YGRVEKVVI
-32==            ---------------GQGNNTTSPPAPFET-GGNTTGISDVT---------VSYQ--VIT
-33=p            ---------------GQGNNTTASQEPFGT-GGNVTSISDVT---------FSYQ--VIT
-34==            SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT
-35=p            SDFN--DSYGLT---GQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLT
-36==            VVPN--TTWW------------QASAPFDTPAALVRAAAK--------------------
-                                                                            
-
-1==             AAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-FTVTMYTSM
-2==             AAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-FTTTLYTSL
-3==             CCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-FTVTFYTAW
-4=p             ALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-FTVTFYTAI
-5=p             AVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-FTVTFYTAI
-6==             SVFMFFIFIGGASINILTILCTIQFKKLRSHLNYILVNLSIANLFVAIFG-SPLSFYSFF
-7==             AAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYILVNVSFGGFLLCIFS-VFPVFVASC
-8=opsin,        ------------------------------------------DLAETVIA-STISIVNQV
-9==             SVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISVVNQV
-10==            SVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIA-STISIVNQV
-11==            SFFMIIVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVA-STISVFNQI
-12==            SVWMIFVVAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIA-STISVINQI
-13==            AVLMGTVVACASVVNGLVIVVSICYKKLRSPLNYILVNLAVADLLVTLCG-SSVSLSNNI
-14==            GTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVK--TPIFIYNSF
-15==            GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIK--TPIFIYNSF
-16==            GVFYIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIF--NSF
-17==            GVFYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLK--APIFIYNSF
-18==            GVIYLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTN-VPFFTYNCF
-19==            GVVYLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTN-FPPFCYNCF
-20==            TAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
-21==            TAYMIMIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
-22==            TAYMIIIGMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITN-TPMMGINLY
-23==            GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFY
-24==            GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQ-SPVMIINFY
-25==            GFVIGMLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCM-SPPMVINCY
-26==            GVAMIILGIICVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFM-MPTMTSNCF
-27==            GIFIGVVGIIGILGNGVVIYLFSKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAF
-28==            GIFIGICGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCF
-29==            GSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
-30==            GSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
-31=p            GSILTLITLLTIAGNCLVVISVSFVKKLRQPSNYLIVSLALADLSVAVAV-MPFVSVTDL
-32==            SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV
-33=p            SLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-LPMAALYQV
-34==            SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI
-35=p            SVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-MPLSVVSEI
-36==            AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-MPLGAVYEV
-                                                          .                 
-
-1==             N-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FRFGNTHAIM
-2==             H-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FRFGENHAIM
-3==             N-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FRFSATHAMM
-4=p             N-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSSHAFA
-5=p             N-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FKFSSTHASA
-6==             N-RYFI--FGATACKIEGFLATLGGMVGLWSLAVVAFERWLVICKPLGN-FTFKTPHAIA
-7==             N-GYFV--FGRHVCALEGFLGTVAGLVTGWSLAFLAFERYIVICKPFGN-FRFSSKHALT
-8=opsin,        S-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLAIV
-9==             Y-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGN-VRFDAKLAIV
-10==            S-GYFV--LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGN-VRFDAKLAIV
-11==            F-GYFI--LGHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGN-IKFDSKLAII
-12==            S-GYFI--LGHPMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGN-IKFDGKLAVA
-13==            N-GFFV--FGRRMCELEGFMVSLTGIVGLWSLAILALERYVVVCKPLGD-FQFQRRHAVS
-14==            H-QGYA--LGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEG--KMTHGKAIA
-15==            H-QGYA--LGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEG--KMTHGKAIA
-16==            H-RGFAIYLGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVI
-17==            H-RGFA--LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNR--NMTFTKAVI
-18==            SGGVWM--FSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNG-PKLTTGKAVV
-19==            SGGRWM--FSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNG-PKLTQGKATF
-20==            F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
-21==            F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
-22==            F-ETWV--LGPMMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAG-RPMTIPLALG
-23==            Y-ETWV--LGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIM
-24==            Y-ETWV--LGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGING-TPMTIKTSIM
-25==            Y-ETWV--LGPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSG-KPLSINGALI
-26==            A-ETWI--LGPFMCEVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAA-APLTHKKATL
-27==            M-KKWI--FGKVACQLYGLLGGIFGFMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFL
-28==            L-KKWI--FGFAACKVYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFI
-29==            IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
-30==            IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
-31=p            IGGKWI--FGHFFCNVFIAMDVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAK
-32==            L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA
-33=p            L-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAA
-34==            S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL
-35=p            S-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRRRSARRILL
-36==            V-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHASTAKRVGM
-                    :   :    * :                  :  :*:  :   :             
-
-1==             GVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNNESYVVYMF
-2==             GVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMF
-3==             GIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHNESYVLYMF
-4=p             GIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNNESYVIYMF
-5=p             GIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNNESYVLYMF
-6==             GCILPWISALAA-SLPPLFG-W-----SRYIPEGLQCSCGPDWYTTNNKYNNESYVMFLF
-7==             VVLATWTIGIGV-SIPPFFG-W-----SRFIPEGLQCSCGPDWYTVGTKYRSESYTWFLF
-8=opsin,        GIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
-9==             GIAFSWIWAAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
-10==            GIAFSWIWSAVW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLM
-11==            GIVFSWVWAWGW-SAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLM
-12==            GILFSWLWSCAW-TAPPIFG-W-----SRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLM
-13==            GCAFTWGWALLW-SAPPLLG-W-----SSYVPEGLRTSCGPNWYTGGSNN--NSYILSLF
-14==            MIIFIYMYATPW-VVACYTETW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIF
-15==            MIIFIYLYATPW-VVACYTESW-----GRFVPEGYLTSCTFDYLT--DNFDTRLFVACIF
-16==            MNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIF
-17==            MNIIIWLYCTPW-VVLPLTQFW-----DRFVPEGYLTSCSFDYLS--DNFDTRLFVGTIF
-18==            FALISWVIAIGC-ALPPFFG-W-----GNYILEGILDSCSYDYLT--QDFNTFSYNIFIF
-19==            MCGLAWVISVGW-SLPPFFG-W-----GSYTLEGILDSCSYDYFT--RDMNTITYNICIF
-20==            KM---------------------------YVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
-21==            KIAYIWFMSSIW-CLAPAFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
-22==            KIAYIWFMSTIWCCLAPVFG-W-----SRYVPEGNLTSCGIDYLE--RDWNPRSYLIFYS
-23==            KILFIWMMAVFW-TVMPLIG-W-----SAYVPEGNLTACSIDYMT--RMWNPRSYLITYS
-24==            KIAFIWMMAVFW-TIMPLIG-W-----SSYVPEGNLTACSIDYMT--RQWNPRSYLITYS
-25==            RIIAIWLFSLGW-TIAPMFG-W-----NRYVPEGNMTACGTDYFN--RGLLSASYLVCYG
-26==            LLLFVWIWSGGW-TILPFFG-W-----SRYVPEGNLTSCTVDYLT--KDWSSASYVVIYG
-27==            MIIFVWMWSIVW-SVGPVFN-W-----GAYVPEGILTSCSFDYLS--TDPSTRSFILCMY
-28==            MIIFVWLWSVLW-AIGPIFG-W-----GAYTLEGVLCNCSFDYIS--RDSTTRSNILCMF
-29==            MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
-30==            MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
-31=p            MILSVWLLSASI-TLPPLFG-W-----AQNVNDDKVCLISQDF----------GYTIYST
-32==            LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST
-33=p            LISLTWLIGFLI-SIPPMLG-WRTPEDRSDPD---ACTISKDH----------GYTIYST
-34==            MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST
-35=p            MIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK----------GYTIFST
-36==            MIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV----------GYQIFAT
-                                                         :                  
-
-1==             VVHFLVPFVIIFFCYGRLLCTV----KEAAAAQQ--------------------------
-2==             VVHFTIPMIVIFFCYGQLVFTV----KEAAAQQQ--------------------------
-3==             VIHFIIPVVVIFFSYGRLICKV----REAAAQQQ--------------------------
-4=p             VCHFILPVAVIFFTYGRLVCTV----KAAAAQQQ--------------------------
-5=p             ICHFILPVTIIFFTYGRLVCTV----KAAAAQQQ--------------------------
-6==             CFCFAVPFGTIVFCYGQLLITL----KLAAKAQA--------------------------
-7==             IFCFIVPLSLICFSYTQLLRAL----KAVAAQQQ--------------------------
-8=opsin,        VTCCITPLSIIVLCYLQVWLAI----RAVAKQQK--------------------------
-9==             VTCCITPLSIIVLCYLQVWLAI----RAVAKQQK--------------------------
-10==            VTCCIIPLAIIMLCYLQVWLAI----RAVAKQQK--------------------------
-11==            ITCCFLPLFIIIVCYLQVWMAI----RAVAAQQK--------------------------
-12==            VTCCFFPLAIIILCYLQVWLAI----RAVAAQQK--------------------------
-13==            VTCFVLPLSLILFSYTNLLLTL----RAAAAQQK--------------------------
-14==            FFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKK-------------------------
-15==            FFSFVCPTTMITYYYSQIVGHVFSHEKALRDQAKK-------------------------
-16==            FFSFVCPTLMILYYYSQIVGHVFSHEKALREQAKK-------------------------
-17==            LFSFVVPTLMILYYYSQIVGHVFNHEKALREQAKK-------------------------
-18==            VFDYFLPAAIIVFSYVFIVKAIFAHEAAMRAQAKK-------------------------
-19==            IFDFFLPASVIVFSYVFIVKAIFAHEAAMRAQAKK-------------------------
-20==            IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
-21==            IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
-22==            IFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKK-------------------------
-23==            LFVYYTPLFLICYSYWFIIAAVAAHEKAMREQAKK-------------------------
-24==            LFVYYTPLFMICYSYWFIIATVAAHEKAMRDQAKK-------------------------
-25==            IWVYFVPLFLIIYSYWFIIQAVAAHEKNMREQAKK-------------------------
-26==            LAVYFLPLITMIYCYFFIVHAVAEHEKQLREQAKK-------------------------
-27==            FCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAKR-------------------------
-28==            ILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR-------------------------
-29==            AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
-30==            AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
-31=p            AVAFYIPMSVMLFMYYQIY-------KAARKSAAKHKF----------------------
-32==            FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------
-33=p            FGAFYIPLLLMLVLYGRIF-------RAARFRIRK-------------------------
-34==            VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY
-35=p            VGAFYLPMLVMMIIYIRIW-------LVARSRIRKDKFQMTKARLKTEETTLVASPKTEY
-36==            ASSFYVPVLIILILYWRIY-------QTARKRIR--------------------------
-                      *   :   *  :                                          
-
-1==             ------------------------------------------------------------
-2==             ------------------------------------------------------------
-3==             ------------------------------------------------------------
-4=p             ------------------------------------------------------------
-5=p             ------------------------------------------------------------
-6==             ------------------------------------------------------------
-7==             ------------------------------------------------------------
-8=opsin,        ------------------------------------------------------------
-9==             ------------------------------------------------------------
-10==            ------------------------------------------------------------
-11==            ------------------------------------------------------------
-12==            ------------------------------------------------------------
-13==            ------------------------------------------------------------
-14==            --------------------------------------------------MN--------
-15==            --------------------------------------------------MN--------
-16==            --------------------------------------------------MN--------
-17==            --------------------------------------------------MN--------
-18==            --------------------------------------------------MN--------
-19==            --------------------------------------------------MN--------
-20==            --------------------------------------------------MN--------
-21==            --------------------------------------------------MN--------
-22==            --------------------------------------------------MN--------
-23==            --------------------------------------------------MN--------
-24==            --------------------------------------------------MN--------
-25==            --------------------------------------------------MN--------
-26==            --------------------------------------------------MN--------
-27==            --------------------------------------------------LN--------
-28==            --------------------------------------------------LN--------
-29==            ---------------------------------PGFPRV----EPDSVIALNG-------
-30==            ---------------------------------PGFPRV----QPESVISLNG-------
-31=p            ---------------------------------PGFPRV----QPESVISLNG-------
-32==            --------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR--
-33=p            --------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG--
-34==            SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---
-35=p            SVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS---
-36==            -------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGIA
-                                                                            
-
-1==             ------------------------------------------------------------
-2==             ------------------------------------------------------------
-3==             ------------------------------------------------------------
-4=p             ------------------------------------------------------------
-5=p             ------------------------------------------------------------
-6==             ------------------------------------------------------------
-7==             ------------------------------------------------------------
-8=opsin,        ------------------------------------------------------------
-9==             ------------------------------------------------------------
-10==            ------------------------------------------------------------
-11==            ------------------------------------------------------------
-12==            ------------------------------------------------------------
-13==            ------------------------------------------------------------
-14==            --VESL------------------------------------------------------
-15==            --VDSL------------------------------------------------------
-16==            --VESL------------------------------------------------------
-17==            --VESL------------------------------------------------------
-18==            --VSTL------------------------------------------------------
-19==            --VTNL------------------------------------------------------
-20==            --VKSL------------------------------------------------------
-21==            --VKSL------------------------------------------------------
-22==            --VKSL------------------------------------------------------
-23==            --VKSL------------------------------------------------------
-24==            --VKSL------------------------------------------------------
-25==            --VASL------------------------------------------------------
-26==            --VASL------------------------------------------------------
-27==            --AKEL------------------------------------------------------
-28==            --AKEL------------------------------------------------------
-29==            --IVKL----------------------QK---------EVEECAN--------------
-30==            --VVKL----------------------QK---------EVEECAN--------------
-31=p            --VVKL----------------------QK---------EVEECAN--------------
-32==            -------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG--
-33=p            -------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG--
-34==            -------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--
-35=p            -------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS--
-36==            AAVVAVIGRPLPTISETTTTGFTNVSS----NNTSP---EKQSCANGLEADPPTTGYGAV
-                                                                            
-
-1==             -------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-H
-2==             -------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-H
-3==             -------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-N
-4=p             -------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-N
-5=p             -------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-N
-6==             -------------DSASTQK------AEREVTKMVVVMVLGFLVCWAPYASFSLWIVS-H
-7==             -------------ESATTQK------AEREVSRMVVVMVGSFCVCYVPYAAFAMYMVN-N
-8=opsin,        -------------ESESTQK------AEKEVTRMVVVMVLAFC-----------------
-9==             -------------ESESTQK------AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAA-N
-10==            -------------ESESTQK------AEKEVTRMVVVMIFAYCVCWGPYTFFACFAAA-N
-11==            -------------ESESTQK------AEREVSRMVVVMIVAFCICWGPYASFVSFAAA-N
-12==            -------------ESESTQK------AEKEVSRMVVVMIVAYCFCWGPYTFFACFAAA-N
-13==            -------------EADTTQR------AEREVTRMVIVMVMAFLLCWLPYSTFALVVAT-H
-14==            ----------RSNVDKNKET------AEIRIAKAAITICFLFFCSWTPYGVMSLIGAF-G
-15==            ----------RSNVDKSKEA------AEIRIAKAAITICFLFFASWTPYGVMSLIGAF-G
-16==            ----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-G
-17==            ----------RSNVDKSKET------AEIRIAKAAITICFLFFVSWTPYGVMSLIGAF-G
-18==            ----------RS-NEADAQR------AEIRIAKTALVNVSLWFICWTPYALISLKGVM-G
-19==            ----------RS-NEAETQR------AEIRIAKTALVNVSLWFICWTPYAAITIQGLL-G
-20==            ----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-K
-21==            ----------RS-SEDAEKS------AEGKLAKVALVTITLWFMAWTPYLVINCMGLF-K
-22==            ----------RS-SEDADKS------AEGKLAKVALVTISLWFMAWTPYLVINCMGLF-K
-23==            ----------RS-SEDCDKS------AEGKLAKVALTTISLWFMAWTPYLVICYFGLF-K
-24==            ----------RS-SEDCDKS------AENKLAKVALTTISLWFMAWTPYLIICYFGLF-K
-25==            ----------RS-SENQNTS------AECKLAKVALMTISLWFMAWTPYLVINFSGIF-N
-26==            ----------RANADQQKQS------AECRLAKVAMMTVGLWFMAWTPYLIISWAGVF-S
-27==            ----------R--KAQAGAS------AEMKLAKISMVIITQFMLSWSPYAIIALLAQF-G
-28==            ----------R--KAQAGAN------AEMRLAKISIVIVSQFLLSWSPYAVVALLAQF-G
-29==            ----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
-30==            ----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
-31=p            ----LSRLLKHERKNISIFK------REQKAATTLGIIVGAFTVCWLPFFLLSTARPFIC
-32==            PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C
-33=p            SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-C
-34==            -----------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V
-35=p            -----------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-V
-36==            AAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-C
-                                           * .           :                  
-
-1==             QGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC--------GKNPL
-2==             QGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC--------GKNPL
-3==             KGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC--------GKNPF
-4=p             KGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC--------GKNPL
-5=p             KGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC--------GKNPL
-6==             RGE--EFDLRMATIPSCLSKASTVYNPVIYVLMNKQFRSCMM-KMVC--------GKN-I
-7==             RNH--GLDLRLVTIPSFFSKSACIYNPIIYCFMNKQFQACIM-KMVC--------GKA-M
-8=opsin,        ------------------------------------------------------------
-9==             PGY--PFHPLMAALPAFFAKSATIYNPVIYVFMNRQFRNCIL-QLF---------GKK-V
-10==            PGY--AFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCIL-QLF---------GKK-V
-11==            PGY--AFHPLAAALPAYFAKSATIYNPVIYVFMNRQFRNCIM-QLF---------GKK-V
-12==            PGY--AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIL-QLF---------GKK-V
-13==            KGI--IIQPVLASLPSYFSKTATVYNPIIYVFMNKQFQSCLL-EMLCCGY----QPQR-T
-14==            DKT--LLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLAL---------N
-15==            DKT--LLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAI---------S
-16==            DKS--LLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGV---------N
-17==            DKS--LLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGV---------N
-18==            DTS--GITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCV------HE-T
-19==            NAE--GITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCV------HE-K
-20==            F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
-21==            F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
-22==            F-E--GLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVF------GK-V
-23==            I-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVF------GN-T
-24==            I-D--GLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVC------GT-T
-25==            L-V--KISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLAC-------A-A
-26==            SGT--RLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLAC------GS-G
-27==            PAE--WVTPYAAELPVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKE-C
-28==            PLE--WVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKE-T
-29==            GTSCSCIPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR----NINR--
-30==            GTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQCQYR----NINR--
-31=p            GTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYR----NINR--
-32==            ESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RQ----
-33=p            ESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC----RR----
-34==            DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--
-35=p            DPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR----RGHR--
-36==            DCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV----RRRR--
-                                                                            
-
-1==             GDDE--SGASTSKTEVSSVS-TSPVSPA--------------------------------
-2==             GDDE--ASATASKTE------TSQVAPA--------------------------------
-3==             GDEDVSSTVSQSKTEVSSVS-SSQVSPA--------------------------------
-4=p             GDDE-SSTVSTSKTEVSS------VSPA--------------------------------
-5=p             GDEE-SSTVSTSKTEVSS------VSPA--------------------------------
-6==             EEDE--ASTSSQVTQVSS------VAPEK-------------------------------
-7==             TDES--DTCSSQKTEVSTVS-STQVGPN--------------------------------
-8=opsin,        ------------------------------------------------------------
-9==             DDGS--ELSSASKTEVSSV---SSVSPA--------------------------------
-10==            DDGS--ELSSASKTEVSSV---SSVSPA--------------------------------
-11==            DDGS--EASTTSRTEVSSVS-NSSVAPA--------------------------------
-12==            DDGS--EVST-SRTEVSSVS-NSSVSPA--------------------------------
-13==            GKAS--PGTPGPHADVTAAGLRNKVMPAHPV-----------------------------
-14==            EKAP--ESSAVASTSTTQEP--QQTTAA--------------------------------
-15==            EKAP--ESRAAISTSTTQEQ--QQTTAA--------------------------------
-16==            EKSG--EISSAQST-TTQEQ--QQTTAA--------------------------------
-17==            EKSG--EASSAQST-TTQEQ-TQQTSAA--------------------------------
-18==            ETKS--NDDSQSNSTVAQDK-A--------------------------------------
-19==            DPND--VEENQSSNTQTQEK-S--------------------------------------
-20==            DDGK--SSDAQSQA-TASEA-ESKA-----------------------------------
-21==            DDGK--SSDAQSQA-TASEA-ESKA-----------------------------------
-22==            DDGK--SSEAQSQA-TTSEA-ESKA-----------------------------------
-23==            DEPK--PDAPASDTETTSEA-DSKA-----------------------------------
-24==            DEPK--PDAPPSDTETTSEA-ESKD-----------------------------------
-25==            EPSS--DAVSTTSGTTTVTD-NEKSNA---------------------------------
-26==            ESGS--DVKSEASATTTMEE-KPKIPEA--------------------------------
-27==            EDAN--DAEEEVVASER--G-GESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGY--PP
-28==            EDDK--DAETEIPAGESSDA-APSADAAQMKEMMAMMQKMQQQQAAY----PPQGYAPPP
-29==            ------KLSAAGMHEALKLAERPERPEF------------VLQNADY-------------
-30==            ------KLSAAGMHEALKLAERPERSEF------------VLQNSDH-------------
-31=p            ------KLSAAGMHEALKLAERPERSEF------------VLQNSDH-------------
-32==            ------------------------------------------------------------
-33=p            ------------------------------------------------------------
-34==            ------------------------------------------------------------
-35=p            ------------------------------------------------------------
-36==            ------A---------------PQ------------------------------------
-                                                                            
-
-1==             ---------------------------------------------------------
-2==             ---------------------------------------------------------
-3==             ---------------------------------------------------------
-4=p             ---------------------------------------------------------
-5=p             ---------------------------------------------------------
-6==             ---------------------------------------------------------
-7==             ---------------------------------------------------------
-8=opsin,        ---------------------------------------------------------
-9==             ---------------------------------------------------------
-10==            ---------------------------------------------------------
-11==            ---------------------------------------------------------
-12==            ---------------------------------------------------------
-13==            ---------------------------------------------------------
-14==            ---------------------------------------------------------
-15==            ---------------------------------------------------------
-16==            ---------------------------------------------------------
-17==            ---------------------------------------------------------
-18==            ---------------------------------------------------------
-19==            ---------------------------------------------------------
-20==            ---------------------------------------------------------
-21==            ---------------------------------------------------------
-22==            ---------------------------------------------------------
-23==            ---------------------------------------------------------
-24==            ---------------------------------------------------------
-25==            ---------------------------------------------------------
-26==            ---------------------------------------------------------
-27==            QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
-28==            QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAYQA
-29==            --------------------------------------------CRKKGHDS-----
-30==            --------------------------------------------CGKKGHDT-----
-31=p            --------------------------------------------CGKKGHDT-----
-32==            ---------------------------------------------------------
-33=p            ---------------------------------------------------------
-34==            ---------------------------------------------------------
-35=p            ---------------------------------------------------------
-36==            ---------------------------------------------------------
-                                                                         
--- a/test-data/sample.fa	Tue Oct 31 15:48:53 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,285 +0,0 @@
->     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
-MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF
-VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG
-GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP
-EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES
-ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL
-YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA
->     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
-MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
-VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
-GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
-EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
-ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI
-YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA
->     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
-MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL
-VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG
-GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP
-EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES
-ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL
-YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA
->     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
-MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV
-VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG
-GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP
-EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS
-ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL
-YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA
->     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
-MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI
-CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG
-GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP
-EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS
-ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL
-YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA
->     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
-MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI
-LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL
-ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS
-RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA
-QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK
-ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK
->     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
-MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL
-RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV
-TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL
-QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT
-QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP
-IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN
->     8=opsin, greensensitive  human (fragment) S07060
-DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP
-FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS
-YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC
->     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
-MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
-IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
-LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
-AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
-QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
-PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
-VSPA
->    10== Z68193   1 human Red Opsin <>[]
-MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
-IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV
-LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS
-AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYL
-QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFH
-PLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
-VSPA
->    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
-MTEAWNVAVFAARRSRDDDDTTRGSVFTYTNTNNTRGPFEGPNYHIAPRWVYNLVSFFMI
-IVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVASTISVFNQIFGYFIL
-GHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNIKFDSKLAIIGIVFSWVWAW
-GWSAPPIFGWSRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQ
-VWMAIRAVAAQQKESESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAANPGYAFHP
-LAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLFGKKVDDGSEASTTSRTEVSSVSNS
-SVAPA
->    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
-MAAWEAAFAARRRHEEEDTTRDSVFTYTNSNNTRGPFEGPNYHIAPRWVYNLTSVWMIFV
-VAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGH
-PMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAW
-TAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVW
-LAIRAVAAQQKESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLA
-AALPAYFAKSATIYNPIIYVFMNRQFRNCILQLFGKKVDDGSEVSTSRTEVSSVSNSSVS
-PA
->    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
-MSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYK
-KLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLW
-SLAILALERYVVVCKPLGDFQFQRRHAVSGCAFTWGWALLWSAPPLLGWSSYVPEGLRTS
-CGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAER
-EVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVF
-MNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV
->    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
-MESGNVSSSLFGNVSTALRPEARLSAETRLLGWNVPPEELRHIPEHWLTYPEPPESMNYL
-LGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVKTPIFIYNSFH
-QGYALGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEGKMTHGKAIAMIIFIY
-MYATPWVVACYTETWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYY
-YSQIVGHVFSHEKALRDQAKKMNVESLRSNVDKNKETAEIRIAKAAITICFLFFCSWTPY
-GVMSLIGAFGDKTLLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLALNE
-KAPESSAVASTSTTQEPQQTTAA
->    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
-MEYHNVSSVLGNVSSVLRPDARLSAESRLLGWNVPPDELRHIPEHWLIYPEPPESMNYLL
-GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIKTPIFIYNSFHQ
-GYALGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEGKMTHGKAIAMIIFIYL
-YATPWVVACYTESWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYYY
-SQIVGHVFSHEKALRDQAKKMNVDSLRSNVDKSKEAAEIRIAKAAITICFLFFASWTPYG
-VMSLIGAFGDKTLLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAISEK
-APESRAAISTSTTQEQQQTTAA
->    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
-MEPLCNASEPPLRPEARSSGNGDLQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGVF
-YIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFNSFHRGFAIY
-LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYCT
-PWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFFFSFVCPTLMILYYYSQI
-VGHVFSHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMS
-LIGAFGDKSLLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGVNEKSGE
-ISSAQSTTTQEQQQTTAA
->    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
-MDALCNASEPPLRPEARMSSGSDELQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGV
-FYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFIYNSFHRGF
-ALGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYC
-TPWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFLFSFVVPTLMILYYYSQ
-IVGHVFNHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVM
-SLIGAFGDKSLLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGVNEKSG
-EASSAQSTTTQEQTQQTSAA
->    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
-MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI
-YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV
-WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV
-IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV
-FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI
-SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET
-KSNDDSQSNSTVAQDKA
->    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
-MANVTGPQMAFYGSGAATFGYPEGMTVADFVPDRVKHMVLDHWYNYPPVNPMWHYLLGVV
-YLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNFPPFCYNCFSGGR
-WMFSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGPKLTQGKATFMCGLAWV
-ISVGWSLPPFFGWGSYTLEGILDSCSYDYFTRDMNTITYNICIFIFDFFLPASVIVFSYV
-FIVKAIFAHEAAMRAQAKKMNVTNLRSNEAETQRAEIRIAKTALVNVSLWFICWTPYAAI
-TIQGLLGNAEGITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCVHEKDP
-NDVEENQSSNTQTQEKS
->    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
-MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
-GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
-MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKMYVPEGNLTSC
-GIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSL
-RSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLFKFEGLTPLNTIWGACFAKS
-AACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDAQSQATASEAESKA
->    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
-MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
-GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
-MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSSIW
-CLAPAFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAA
-VSAHEKAMREQAKKMNVKSLRSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGL
-FKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDA
-QSQATASEAESKA
->    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
-MDSFAAVATQLGPQFAAPSNGSVVDKVTPDMAHLISPYWDQFPAMDPIWAKILTAYMIII
-GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
-MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSTIW
-CCLAPVFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIA
-AVSAHEKAMREQAKKMNVKSLRSSEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMG
-LFKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSE
-AQSQATTSEAESKA
->    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
-MERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKIL
-GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
-ETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFI
-WMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYS
-YWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYL
-VICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTD
-EPKPDAPASDTETTSEADSKA
->    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
-MERSLLPEPPLAMALLGPRFEAQTGGNRSVLDNVLPDMAPLVNPHWSRFAPMDPTMSKIL
-GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
-ETWVLGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIAFI
-WMMAVFWTIMPLIGWSSYVPEGNLTACSIDYMTRQWNPRSYLITYSLFVYYTPLFMICYS
-YWFIIATVAAHEKAMRDQAKKMNVKSLRSSEDCDKSAENKLAKVALTTISLWFMAWTPYL
-IICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVCGTTD
-EPKPDAPPSDTETTSEAESKD
->    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
-MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG
-MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL
-GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL
-GWTIAPMFGWNRYVPEGNMTACGTDYFNRGLLSASYLVCYGIWVYFVPLFLIIYSYWFII
-QAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVINFS
-GIFNLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSSDAV
-STTSGTTTVTDNEKSNA
->    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
-MANQLSYSSLGWPYQPNASVVDTMPKEMLYMIHEHWYAFPPMNPLWYSILGVAMIILGII
-CVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFMMPTMTSNCFAETWILGPFMC
-EVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAAPLTHKKATLLLLFVWIWSGGWTIL
-PFFGWSRYVPEGNLTSCTVDYLTKDWSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAE
-HEKQLREQAKKMNVASLRANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVFS
-SGTRLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLACGSGESGSDVKSE
-ASATTTMEEKPKIPEA
->    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
-MVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLF
-SKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFG
-FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVP
-EGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAK
-RLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAEL
-PVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASER
-GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPP
-QGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
->    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
-MGRDLRDNETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFT
-KTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGF
-MSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLE
-GVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR
-LNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLP
-VMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGESS
-DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGY
-PPPPQGAPPQGAPPAAPPQGVDNQAYQA
->    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
-MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSEVTASPAPTW
-DAPPDNASGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLI
-VSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAMDVMCCTASIMTLCVISIDR
-YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT
-IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE
-ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC
-IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK
-LAERPERPEFVLQNADYCRKKGHDS
->    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
-MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
-VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
-DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
-AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
-QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
-PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC
-QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
->    31=p A47425 serotonin receptor 5HT-7 - rat
-MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
-VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
-DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
-AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
-QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
-PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC
-QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
->    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
-MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA
-IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
-RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT
-RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN
-SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
-FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
-RQ
->    33=p A35181 serotonin receptor class 1A - rat
-MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA
-IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
-TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
-RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT
-SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN
-SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
-FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
-RR
->    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
-MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
-HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
-MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
-ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
-DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
-ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
-NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
-LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
-NPIIYTIFSPEFRSAFQKILFGKYRRGHR
->    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
-MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
-HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
-MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
-ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
-DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
-ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
-NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
-LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
-NPIIYTIFSPEFRSAFQKILFGKYRRGHR
->    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
-MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR
-AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV
-YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM
-IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI
-LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI
-SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR
-ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT
-VFSPEFRHAFQRLLCGRRVRRRRAPQ
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_amino.fa	Wed Mar 20 07:34:52 2024 +0000
@@ -0,0 +1,285 @@
+>     1== M63632   1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]
+MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF
+VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG
+GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP
+EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES
+ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL
+YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA
+>     2== U22180   1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]
+MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
+VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
+GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
+EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES
+ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI
+YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA
+>     3== M92038   1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9
+MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL
+VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG
+GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP
+EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES
+ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL
+YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA
+>     4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish
+MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV
+VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP
+EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL
+YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA
+>     5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish
+MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI
+CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG
+GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP
+EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS
+ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL
+YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA
+>     6== L11864   1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-
+MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI
+LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL
+ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS
+RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA
+QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK
+ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK
+>     7== M13299   1 human BCP <>[Science232(4747),193-202'86]
+MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL
+RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV
+TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL
+QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT
+QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP
+IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN
+>     8=opsin, greensensitive  human (fragment) S07060
+DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP
+FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS
+YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC
+>     9== K03494   1 human GCP <>[Science232(4747),193-202'86]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
+PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+>    10== Z68193   1 human Red Opsin <>[]
+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
+IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV
+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS
+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYL
+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFH
+PLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
+VSPA
+>    11== M92036   1 Gecko gecko P521 <retina>[PNAS89,6841-6845'92]
+MTEAWNVAVFAARRSRDDDDTTRGSVFTYTNTNNTRGPFEGPNYHIAPRWVYNLVSFFMI
+IVVIASCFTNGLVLVATAKFKKLRHPLNWILVNLAFVDLVETLVASTISVFNQIFGYFIL
+GHPLCVIEGYVVSSCGITGLWSLAIISWERWFVVCKPFGNIKFDSKLAIIGIVFSWVWAW
+GWSAPPIFGWSRYWPHGLKTSCGPDVFSGSVELGCQSFMLTLMITCCFLPLFIIIVCYLQ
+VWMAIRAVAAQQKESESTQKAEREVSRMVVVMIVAFCICWGPYASFVSFAAANPGYAFHP
+LAAALPAYFAKSATIYNPVIYVFMNRQFRNCIMQLFGKKVDDGSEASTTSRTEVSSVSNS
+SVAPA
+>    12== M62903   1 chicken visual pigment <>[BBRC173,1212-1217'90]
+MAAWEAAFAARRRHEEEDTTRDSVFTYTNSNNTRGPFEGPNYHIAPRWVYNLTSVWMIFV
+VAASVFTNGLVLVATWKFKKLRHPLNWILVNLAVADLGETVIASTISVINQISGYFILGH
+PMCVVEGYTVSACGITALWSLAIISWERWFVVCKPFGNIKFDGKLAVAGILFSWLWSCAW
+TAPPIFGWSRYWPHGLKTSCGPDVFSGSSDPGVQSYMVVLMVTCCFFPLAIIILCYLQVW
+LAIRAVAAQQKESESTQKAEKEVSRMVVVMIVAYCFCWGPYTFFACFAAANPGYAFHPLA
+AALPAYFAKSATIYNPIIYVFMNRQFRNCILQLFGKKVDDGSEVSTSRTEVSSVSNSSVS
+PA
+>    13== S75720   1 chicken P-opsin <>[Science267(5203),1502-1506'95]
+MSSNSSQAPPNGTPGPFDGPQWPYQAPQSTYVGVAVLMGTVVACASVVNGLVIVVSICYK
+KLRSPLNYILVNLAVADLLVTLCGSSVSLSNNINGFFVFGRRMCELEGFMVSLTGIVGLW
+SLAILALERYVVVCKPLGDFQFQRRHAVSGCAFTWGWALLWSAPPLLGWSSYVPEGLRTS
+CGPNWYTGGSNNNSYILSLFVTCFVLPLSLILFSYTNLLLTLRAAAAQQKEADTTQRAER
+EVTRMVIVMVMAFLLCWLPYSTFALVVATHKGIIIQPVLASLPSYFSKTATVYNPIIYVF
+MNKQFQSCLLEMLCCGYQPQRTGKASPGTPGPHADVTAAGLRNKVMPAHPV
+>    14== M17718   1 D.melanogaster Rh3 <>[J.Neurosci.7,1550-1557'87]
+MESGNVSSSLFGNVSTALRPEARLSAETRLLGWNVPPEELRHIPEHWLTYPEPPESMNYL
+LGTLYIFFTLMSMLGNGLVIWVFSAAKSLRTPSNILVINLAFCDFMMMVKTPIFIYNSFH
+QGYALGHLGCQIFGIIGSYTGIAAGATNAFIAYDRFNVITRPMEGKMTHGKAIAMIIFIY
+MYATPWVVACYTETWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYY
+YSQIVGHVFSHEKALRDQAKKMNVESLRSNVDKNKETAEIRIAKAAITICFLFFCSWTPY
+GVMSLIGAFGDKTLLTPGATMIPACACKMVACIDPFVYAISHPRYRMELQKRCPWLALNE
+KAPESSAVASTSTTQEPQQTTAA
+>    15== X65879   1 Drosophila pseudoobscura Dpse\Rh3 <>[Genetics132(1),193-204'92
+MEYHNVSSVLGNVSSVLRPDARLSAESRLLGWNVPPDELRHIPEHWLIYPEPPESMNYLL
+GTLYIFFTVISMIGNGLVMWVFSAAKSLRTPSNILVINLAFCDFMMMIKTPIFIYNSFHQ
+GYALGHLGCQIFGVIGSYTGIAAGATNAFIAYDRYNVITRPMEGKMTHGKAIAMIIFIYL
+YATPWVVACYTESWGRFVPEGYLTSCTFDYLTDNFDTRLFVACIFFFSFVCPTTMITYYY
+SQIVGHVFSHEKALRDQAKKMNVDSLRSNVDKSKEAAEIRIAKAAITICFLFFASWTPYG
+VMSLIGAFGDKTLLTPGATMIPACTCKMVACIDPFVYAISHPRYRMELQKRCPWLAISEK
+APESRAAISTSTTQEQQQTTAA
+>    16== M17730   1 D.melanogaster Rh4 opsin <>[J.Neurosci.7,1558-1566'87]
+MEPLCNASEPPLRPEARSSGNGDLQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGVF
+YIFLFCASTVGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFNSFHRGFAIY
+LGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYCT
+PWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFFFSFVCPTLMILYYYSQI
+VGHVFSHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVMS
+LIGAFGDKSLLTQGATMIPACTCKLVACIDPFVYAISHPRYRLELQKRCPWLGVNEKSGE
+ISSAQSTTTQEQQQTTAA
+>    17== X65880   1 Drosophila pseudoobscura Dpse\Rh4 <>[Genetics132(1),193-204'92
+MDALCNASEPPLRPEARMSSGSDELQFLGWNVPPDQIQYIPEHWLTQLEPPASMHYMLGV
+FYIFLFFASTLGNGMVIWIFSTSKSLRTPSNMFVLNLAVFDLIMCLKAPIFIYNSFHRGF
+ALGNTWCQIFASIGSYSGIGAGMTNAAIGYDRYNVITKPMNRNMTFTKAVIMNIIIWLYC
+TPWVVLPLTQFWDRFVPEGYLTSCSFDYLSDNFDTRLFVGTIFLFSFVVPTLMILYYYSQ
+IVGHVFNHEKALREQAKKMNVESLRSNVDKSKETAEIRIAKAAITICFLFFVSWTPYGVM
+SLIGAFGDKSLLTPGATMIPACTCKLVACIEPFVYAISHPRYRMELQKRCPWLGVNEKSG
+EASSAQSTTTQEQTQQTSAA
+>    18== D50584   1 Hemigrapsus sanguineus opsin BcRh2 <compound eye>[J.Exp.Biol.1
+MTNATGPQMAYYGAASMDFGYPEGVSIVDFVRPEIKPYVHQHWYNYPPVNPMWHYLLGVI
+YLFLGTVSIFGNGLVIYLFNKSAALRTPANILVVNLALSDLIMLTTNVPFFTYNCFSGGV
+WMFSPQYCEIYACLGAITGVCSIWLLCMISFDRYNIICNGFNGPKLTTGKAVVFALISWV
+IAIGCALPPFFGWGNYILEGILDSCSYDYLTQDFNTFSYNIFIFVFDYFLPAAIIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVSTLRSNEADAQRAEIRIAKTALVNVSLWFICWTPYALI
+SLKGVMGDTSGITPLVSTLPALLAKSCSCYNPFVYAISHPKYRLAITQHLPWFCVHETET
+KSNDDSQSNSTVAQDKA
+>    19== D50583   1 Hemigrapsus sanguineus opsin BcRh1 <compound eye>[J.Exp.Biol.1
+MANVTGPQMAFYGSGAATFGYPEGMTVADFVPDRVKHMVLDHWYNYPPVNPMWHYLLGVV
+YLFLGVISIAGNGLVIYLYMKSQALKTPANMLIVNLALSDLIMLTTNFPPFCYNCFSGGR
+WMFSGTYCEIYAALGAITGVCSIWTLCMISFDRYNIICNGFNGPKLTQGKATFMCGLAWV
+ISVGWSLPPFFGWGSYTLEGILDSCSYDYFTRDMNTITYNICIFIFDFFLPASVIVFSYV
+FIVKAIFAHEAAMRAQAKKMNVTNLRSNEAETQRAEIRIAKTALVNVSLWFICWTPYAAI
+TIQGLLGNAEGITPLLTTLPALLAKSCSCYNPFVYAISHPKFRLAITQHLPWFCVHEKDP
+NDVEENQSSNTQTQEKS
+>    20== K02320   1 D.melanogaster opsin <>[Cell40,851-858'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKMYVPEGNLTSC
+GIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAAVSAHEKAMREQAKKMNVKSL
+RSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGLFKFEGLTPLNTIWGACFAKS
+AACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDAQSQATASEAESKA
+>    21== K02315   1 D.melanogaster ninaE <>[Cell40,839-850'85]
+MESFAVAAAQLGPHFAPLSNGSVVDKVTPDMAHLISPYWNQFPAMDPIWAKILTAYMIMI
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSSIW
+CLAPAFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIAA
+VSAHEKAMREQAKKMNVKSLRSSEDAEKSAEGKLAKVALVTITLWFMAWTPYLVINCMGL
+FKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSDA
+QSQATASEAESKA
+>    22== X65877   1 Drosophila pseudoobscura Dpse\ninaE <>[Genetics132(1),193-204'
+MDSFAAVATQLGPQFAAPSNGSVVDKVTPDMAHLISPYWDQFPAMDPIWAKILTAYMIII
+GMISWCGNGVVIYIFATTKSLRTPANLLVINLAISDFGIMITNTPMMGINLYFETWVLGP
+MMCDIYAGLGSAFGCSSIWSMCMISLDRYQVIVKGMAGRPMTIPLALGKIAYIWFMSTIW
+CCLAPVFGWSRYVPEGNLTSCGIDYLERDWNPRSYLIFYSIFVYYIPLFLICYSYWFIIA
+AVSAHEKAMREQAKKMNVKSLRSSEDADKSAEGKLAKVALVTISLWFMAWTPYLVINCMG
+LFKFEGLTPLNTIWGACFAKSAACYNPIVYGISHPKYRLALKEKCPCCVFGKVDDGKSSE
+AQSQATTSEAESKA
+>    23== M12896   1 D.melanogaster Rh2 <>[Cell44,705-710'86]
+MERSHLPETPFDLAHSGPRFQAQSSGNGSVLDNVLPDMAHLVNPYWSRFAPMDPMMSKIL
+GLFTLAIMIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAGCGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKILFI
+WMMAVFWTVMPLIGWSAYVPEGNLTACSIDYMTRMWNPRSYLITYSLFVYYTPLFLICYS
+YWFIIAAVAAHEKAMREQAKKMNVKSLRSSEDCDKSAEGKLAKVALTTISLWFMAWTPYL
+VICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPKYRIVLKEKCPMCVFGNTD
+EPKPDAPASDTETTSEADSKA
+>    24== X65878   1 Drosophila pseudoobscura Dpse\Rh2 <>[Genetics132(1),193-204'92
+MERSLLPEPPLAMALLGPRFEAQTGGNRSVLDNVLPDMAPLVNPHWSRFAPMDPTMSKIL
+GLFTLVILIISCCGNGVVVYIFGGTKSLRTPANLLVLNLAFSDFCMMASQSPVMIINFYY
+ETWVLGPLWCDIYAACGSLFGCVSIWSMCMIAFDRYNVIVKGINGTPMTIKTSIMKIAFI
+WMMAVFWTIMPLIGWSSYVPEGNLTACSIDYMTRQWNPRSYLITYSLFVYYTPLFMICYS
+YWFIIATVAAHEKAMRDQAKKMNVKSLRSSEDCDKSAENKLAKVALTTISLWFMAWTPYL
+IICYFGLFKIDGLTPLTTIWGATFAKTSAVYNPIVYGISHPNDRLVLKEKCPMCVCGTTD
+EPKPDAPPSDTETTSEAESKD
+>    25== U26026   1 Apis mellifera long-wavelength rhodopsin <>[]
+MIAVSGPSYEAFSYGGQARFNNQTVVDKVPPDMLHLIDANWYQYPPLNPMWHGILGFVIG
+MLGFVSAMGNGMVVYIFLSTKSLRTPSNLFVINLAISNFLMMFCMSPPMVINCYYETWVL
+GPLFCQIYAMLGSLFGCGSIWTMTMIAFDRYNVIVKGLSGKPLSINGALIRIIAIWLFSL
+GWTIAPMFGWNRYVPEGNMTACGTDYFNRGLLSASYLVCYGIWVYFVPLFLIIYSYWFII
+QAVAAHEKNMREQAKKMNVASLRSSENQNTSAECKLAKVALMTISLWFMAWTPYLVINFS
+GIFNLVKISPLFTIWGSLFAKANAVYNPIVYGISHPKYRAALFAKFPSLACAAEPSSDAV
+STTSGTTTVTDNEKSNA
+>    26== L03781   1 Limulus polyphemus opsin <>[PNAS90,6150-6154'93]
+MANQLSYSSLGWPYQPNASVVDTMPKEMLYMIHEHWYAFPPMNPLWYSILGVAMIILGII
+CVLGNGMVIYLMMTTKSLRTPTNLLVVNLAFSDFCMMAFMMPTMTSNCFAETWILGPFMC
+EVYGMAGSLFGCASIWSMVMITLDRYNVIVRGMAAAPLTHKKATLLLLFVWIWSGGWTIL
+PFFGWSRYVPEGNLTSCTVDYLTKDWSSASYVVIYGLAVYFLPLITMIYCYFFIVHAVAE
+HEKQLREQAKKMNVASLRANADQQKQSAECRLAKVAMMTVGLWFMAWTPYLIISWAGVFS
+SGTRLTPLATIWGSVFAKANSCYNPIVYGISHPRYKAALYQRFPSLACGSGESGSDVKSE
+ASATTTMEEKPKIPEA
+>    27== X07797   1 Octopus dofleini rhodopsin <>[FEBS232(1),69-72'88]
+MVESTTLVNQTWWYNPTVDIHPHWAKFDPIPDAVYYSVGIFIGVVGIIGILGNGVVIYLF
+SKTKSLQTPANMFIINLAMSDLSFSAINGFPLKTISAFMKKWIFGKVACQLYGLLGGIFG
+FMSINTMAMISIDRYNVIGRPMAASKKMSHRRAFLMIIFVWMWSIVWSVGPVFNWGAYVP
+EGILTSCSFDYLSTDPSTRSFILCMYFCGFMLPIIIIAFCYFNIVMSVSNHEKEMAAMAK
+RLNAKELRKAQAGASAEMKLAKISMVIITQFMLSWSPYAIIALLAQFGPAEWVTPYAAEL
+PVLFAKASAIHNPIVYSVSHPKFREAIQTTFPWLLTCCQFDEKECEDANDAEEEVVASER
+GGESRDAAQMKEMMAMMQKMQAQQAAYQPPPPPQGYPPQGYPPQGAYPPPQGYPPQGYPP
+QGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAYQA
+>    28== X70498   1 Todarodes pacificus rhodopsin <retina>[FEBS317(1-2),5-11'93]
+MGRDLRDNETWWYNPSIVVHPHWREFDQVPDAVYYSLGIFIGICGIIGCGGNGIVIYLFT
+KTKSLQTPANMFIINLAFSDFTFSLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGF
+MSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWSVLWAIGPIFGWGAYTLE
+GVLCNCSFDYISRDSTTRSNILCMFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKR
+LNAKELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALLAQFGPLEWVTPYAAQLP
+VMFAKASAIHNPMIYSVSHPKFREAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGESS
+DAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGY
+PPPPQGAPPQGAPPAAPPQGVDNQAYQA
+>    29== L21195   1 human serotonin 5-HT7 receptor protein <placenta and fetal bra
+MMDVNSSGRPDLYGHLRSFLLPEVGRGLPDLSPDGGADPVAGSWAPHLLSEVTASPAPTW
+DAPPDNASGCGEQINYGRVEKVVIGSILTLITLLTIAGNCLVVISVCFVKKLRQPSNYLI
+VSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAMDVMCCTASIMTLCVISIDR
+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT
+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE
+ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC
+IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK
+LAERPERPEFVLQNADYCRKKGHDS
+>    30== L15228   1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+>    31=p A47425 serotonin receptor 5HT-7 - rat
+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL
+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM
+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW
+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV
+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL
+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC
+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT
+>    32== M83181   1 human serotonin receptor <>[JBC267(11),7553-7562'92]
+MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT
+RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN
+SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RQ
+>    33=p A35181 serotonin receptor class 1A - rat
+MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA
+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC
+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED
+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT
+SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN
+SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP
+FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC
+RR
+>    34== L06803   1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+>    35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail
+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS
+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV
+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT
+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP
+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE
+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA
+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK
+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL
+NPIIYTIFSPEFRSAFQKILFGKYRRGHR
+>    36== X95604   1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi
+MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR
+AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV
+YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM
+IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI
+LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI
+SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR
+ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT
+VFSPEFRHAFQRLLCGRRVRRRRAPQ
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_nuc.fa	Wed Mar 20 07:34:52 2024 +0000
@@ -0,0 +1,41 @@
+>MZ681498.1 Rotylenchus bunae isolate GE29E-RO6 small subunit ribosomal RNA gene, partial sequence
+ATGCATGTATAAGTATAACCTGCCAGACAGGGAAACTGCGGACGGCTCATTACAACAGCCTTAATTTACT
+TGACCTTGACAACCTACTTGGATAACTGCGGTAATTCTGGAGCTAATACATGCACCAAAGCTCCGATCCC
+TCGTGGAGAGGAGCGCATTTGTTCGCCACAAAACCAAACGCCCCACAAGGGCGTTCAGTGTTGACTCAGA
+ATAACTAAGCTGATCGCACGGTCTTGCACCGGCGACGTGTCTTTCAAGTGTCTGCCTTATCAACTTTCGA
+TGGTAGTGTATCTGCCTACCATGGTTGTGACGGGTAACGGAGGATAAGGGTTCGACTCCGGAGAAGGGGC
+CTGAGAAATGGCCACTACGTCTAAGGATGGCAGCAGGCGCGCAAATTACCCACTCTCAACACGCTGAGGA
+GGTAGTGAAGAGAAATAACGAGACCGTTCTCACATGAGGCCGGTCATCGGAATGGGTACAACTTAAACCC
+TTTAACGAGTATCTATGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCAAAATGCAT
+AGAATTATTGCTGCGGTTAAAAAGCTCGTAGTTGGATCTGTGCTGGCCGCCCGGTCTGCTCGCTGAGCAC
+GCACTGGTGCGGTCGGCTTTCCTGCCCGGTACCTCCCCGGCGTTGGCCTTCACCGGTCGGCGTCGGTGGC
+CGGGCGAGTTTACTTTGAACAAATCAGAGTGCTTCAAACAGGCGTTTCGCTTGAATGTTCGTGCATGGAA
+TAATAGAAGAGGATTTCGGTCCGATTTTGTTGGTTTTGCTGACCGAGATAATGGTTAACAGAGACAAACG
+GGGCCATTCGTATTGCTACGTGAGAGGTG
+
+>MZ681497.1 Rotylenchus bunae isolate GE29A-R1 small subunit ribosomal RNA gene, partial sequence
+CTGCGGACGGCTCATTACAACAGCCTTAATTTACTTGACCTTGACAACCTACTTGGATAACTGCGGTAAT
+TCTGGAGCTAATACATGCACCAAAGCTCCGATCCCTCGTGGAGAGGAGCGCATTTGTTCGCCACAAAACC
+AAACGCCCCACAAGGGCGTTCAGTGTTGACTCAGAATAACTAAGCTGATCGCACGGTCTTGCACCGGCGA
+CGTGTCTTTCAAGTGTCTGCCTTATCAACTTTCGATGGTAGTGTATCTGCCTACCATGGTTGTGACGGGT
+AACGGAGGATAAGGGTTCGACTCCGGAGAAGGGGCCTGAGAAATGGCCACTACGTCTAAGGATGGCAGCA
+GGCGCGCAAATTACCCACTCTCAACACGCTGAGGAGGTAGTGAAGAGAAATAACGAGACCGTTCTCACAT
+GAGGCCGGTCATCGGAATGGGTACAACTTAAACCCTTTAACGAGTATCTATGAGAGGGCAAGTCTGGTGC
+CAGCAGCCGCGGTAATTCCAGCTCTCAAAATGCATAGAATTATTGCTGCGGTTAAAAAGCTCGTAGTTGG
+ATCTGTGCTGGCCGCCCGGTCTGCTCGCTGAGCACGCACTGGTGCGGTCGGCTTTCCTGCCCGGTACCTC
+CCCGGCGTTGGCCTTCACCGGTCGGCGTCGGTGGCCGGGCGAGTTTACTTTGAACAAATCAGAGTGCTTC
+AAACAGGCGTTTCGCTTGAATGTTCGTGCATGGAATAATAGAAGAGGATTTCGGTCCGATTTTGTTGGTT
+TTGCTGACCGAGATAATGGTTAACAGAGACAAACGGGGCCATTCGTATTGCTACGTGAGAGGTGAAATTC
+TTGGACCGTAGCAAGACGGACTACAGC
+
+>ON855043.1 Rotylenchus sp. JQ-2022 internal transcribed spacer 1 and 5.8S ribosomal RNA gene, partial sequence
+GGCCGTCACTCCGGGGGGACAACACAAACGCCCTGAGGGCTTTACTCGTTGGGGTGCAAACTGGATCGAG
+TGGCGCACACATCCCTTCCACGCAAAGACCTGCTGAAGAGGTCGGAGGCGATGAGTCCGAGCAACCCCAC
+AAGCAACCAGGTTGGGGAAGCTGCACACGATACTGGGATGCACGCCCCCAGGGCACCTAACGGCTGCCGC
+TGGCGTCTGTGCGTCGTTGAGCAGTTGTTGCGCACTTGCTTTTGTCGGAGCTGTACTCGGAGCATGCTGG
+CATGGACCCACACAAAAGTGTGTGGCAGCGGCCACACACCCCTGTCCATGTCCTACGGACCGTAGCTAGG
+GCGTGCTCTGGGTTTCTTCGGCTGGCAGTGTTGCTACGTCCGTGGCTGTGATGAGACGACGCGGTAGGGC
+CTTGTGCGATGCGCCTGCACTTGGCTTAAGACTTGATGAGCTCACTGCGAAGAGCCGCCAGCAACCTTTT
+TTTCATATACATTTTTTACAGGCACACTTGTGTGCTGATGAACAAAAATTCTAGCCTTATCGGTGGATCA
+CTCGGCTCGTAGGTCGATG
+