Mercurial > repos > abims-sbr > blastalign
changeset 0:d0ae18156aa2 draft default tip
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BlastAlign.xml Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,236 @@ +<tool name="BlastAlign" id="blastalign" version="2.1"> + + <description> + Align the nucleic acid sequences using BLASTN + </description> + + <macros> + <import>macros.xml</import> + </macros> + + <requirements> + <expand macro="python_required" /> + <requirement type="package" version="1.4">blastalign</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command><![CDATA[ + ln -s '$input' '$input.element_identifier'".fasta" && + + BlastAlign -i '$input.element_identifier'".fasta" + -m $advanced_option.m + #if $advanced_option.r != "" + -r $advanced_option.r + #end if + #if $advanced_option.x != "" + -x $advanced_option.x + #end if + -n $advanced_option.n + #if $advanced_option.s != 0 + -s $advanced_option.s + #end if + && + ln -s '$input.element_identifier'".fasta.phy" out.phy && + ln -s '$input.element_identifier'".fasta.nxs" out.nxs + #if $output_format.value == "fasta" + && python $__tool_directory__/scripts/S01_phylip2fasta.py out.phy out.fasta + #end if + + ]]></command> + <inputs> + <param name="input" type="data" format="fasta" label="Choose your file" help="A fasta file with nucleotides sequences" /> + + <section name="advanced_option" title="Blast advanced options" expanded="True"> + <param argument="-m" type="integer" value="95" min="0" max="100" label="Proportion of gaps allowed in any one sequence in the final alignement" help="default = 95, i.e. only removing sequences with extremely short matches" /> + <param argument="-r" type="text" area="True" size="1x20" label="Choose a reference sequence" help="default is to search for best candidate (if entered, the sequence will be extracted, written to a separate file, and blasted against the original input file)"/> + <param argument="-x" type="text" area="True" size="5x25" label="Choose the sequences to be excluded from this analysis" help="name of comma-separated sequences " /> + <param argument="-n" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Retain original names in output files" help="option F is to output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the program" /> + <param argument="-s" type="integer" value="0" min="0" label="Number of sequences to be used in initial search for reference sequence" help="default (= 0) is to find the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large" /> + </section> + + <param name="output_format" type="select" label="Output format" help="phylip, nexus, or fasta." > + <option value="fasta">fasta</option> + <option value="phylip">phylip</option> + <option value="nexus">nexus</option> + </param> + </inputs> + + <outputs> + <data format="phylip" name="phy" from_work_dir="out.phy" label="Blastalign on ${input.name} in phylip"> + <filter>output_format == "phylip"</filter> + </data> + <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Blastalign on ${input.name} in nexus"> + <filter>output_format == "nexus"</filter> + </data> + <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Blastalign on ${input.name} in fasta"> + <filter>output_format == "fasta"</filter> + </data> + </outputs> + + <tests> + <test> + <param name="input" ftype="fasta" value="inputs/locus1_sp2.fasta" /> + <section name="advanced_option"> + <param name="m" value="95" /> + <param name="r" value="" /> + <param name="x" value="" /> + <param name="n" value="False" /> + <param name="s" value="0" /> + </section> + <param name="output_format" value="fasta" /> + <output name="fasta" value="outputs/locus1_sp2.fasta" /> + </test> + <test> + <param name="input" ftype="fasta" value="inputs/locus1_sp3.fasta" /> + <section name="advanced_option"> + <param name="m" value="95" /> + <param name="r" value="" /> + <param name="x" value="" /> + <param name="n" value="False" /> + <param name="s" value="0" /> + </section> + <param name="output_format" value="phylip" /> + <output name="phy" value="outputs/locus1_sp3.phy" /> + </test> + <test> + <param name="input" ftype="fasta" value="inputs/locus3_sp2.fasta" /> + <section name="advanced_option"> + <param name="m" value="95" /> + <param name="r" value="" /> + <param name="x" value="" /> + <param name="n" value="False" /> + <param name="s" value="0" /> + </section> + <param name="output_format" value="nexus" /> + <output name="nxs" value="outputs/locus3_sp2.nxs" /> + </test> + <!-- + <test> + <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" /> + <section name="advanced_option"> + <param name="m" value="95" /> + <param name="r" value="" /> + <param name="x" value="" /> + <param name="n" value="False" /> + <param name="s" value="0" /> + </section> + <param name="output_format" value="phylip" /> + <output name="phy" value="outputs/locus8_sp2.phy" /> + </test> + --> + <test> + <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" /> + <section name="advanced_option"> + <param name="m" value="95" /> + <param name="r" value="" /> + <param name="x" value="" /> + <param name="n" value="False" /> + <param name="s" value="0" /> + </section> + <param name="output_format" value="fasta" /> + <output name="phy" value="outputs/locus8_sp2.fasta" /> + </test> + + <!--locus10_sp2.fasta locus1_sp3.fasta locus2_sp2.fasta locus3_sp2.fasta locus4_sp2.fasta locus5_sp2.fasta locus6_sp2.fasta locus7_sp2.fasta locus8_sp2.fasta locus9_sp2.fasta--> + </tests> + + <help> + <![CDATA[ + +.. class:: infomark + +**Authors** BlastAlign has been written by Robert Belshaw and Aris Katzourakis. + +.. class:: infomark + +**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station + + | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + | Credits : Gildas le Corguillé, Misharl Monsoor, Victor Mataigne + +-------- + +**Description** + +BlastAlign takes a set of nucleic sequences in a file in fasta format and returns a multiple alignment (in Nexus and Phylip formats) using BLAST+. This Galaxy implementation works with dataset collections, which allows multiple parallels runs of BlastAlign at once on many files. + +-------- + +**Parameters** + +The choice of several parameters for the blast is possible. + +**-m : Proportion of gaps allowed in any one sequence in the final alignement** + integer (between 0 and 100). + By default : 95%, i.e. only removes sequences with extremely short matches. + We find 50 the most useful. + +**-r : Name of reference sequence** + text. + Default is searching for best candidate. + If entered, the sequence will be extracted, written to a separate file, and blasted against the original input file. + + **-x : Name of sequences to be excluded from the analysis** + text. + names must be comma-separated. + + **-n** + If checked : retain original names in output files. + If not checked : output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the tool. + Default : checked. + +**-s : Number of sequences to be used in initial search for reference sequence** + integer (between 0 and total number of sequences). + Default : 0 + Default is finding the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large. + +** Output format :** + The user have the choice between three format (only one is returned per run) : fasta, phylip, and nexus. + +-------- + +**Outputs** + +The output format is + + - 'Blastalign_on_{input.name}_phylip' : + the aligned sequences in Phylip format. + + - 'Blastalign_on_{input.name}_nexus' : + the aligned sequences in Nexus format. + + - 'Blastalign_on_{input_file}_fasta' : + the aligned sequences in Fasta format if the option "fasta format" is checked. + +--------- + +Changelog +--------- + +**Version 2.1 - 17/01/2018** + + - New parameter "output format" + - Applied some bugfixes and minor improvments + +**Version 2.0 - 21/04/2017** + + - NEW: BlastAlign will now be launched on one file at once. Although, it will manage a Dataset Collection to deal with numerous files. + +**Version 1.0 - 13/04/2017** + + - TEST: Add funtional test with planemo + - IMPROVEMENT: Use conda dependencies for blastalign, blast-legacy, perl, python + + ]]> + + </help> + + <citations> + <citation type="doi">10.1093/bioinformatics/bth459</citation> + </citations> + +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,14 @@ +Changelog +--------- + +**Version 2.0 - 21/04/2017** + + - NEW: BlastAlign will now be launched on one file at once. Although, it will manage a Dataset Collection to deal with numerous files. + + +**Version 1.0 - 13/04/2017** + + - TEST: Add funtional test with planemo + + - IMPROVEMENT: Use conda dependencies for blastalign, blast-legacy, perl, python +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,32 @@ +<macros> + + <xml name="python_required"> + <requirement type="package" version="2.7">python</requirement> + </xml> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2. + +.. class:: infomark + +**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station + + | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + | Credits : Gildas le Corguillé, Misharl Monsoor + +--------------------------------------------------- + + </token> + + <xml name="citations"> + <citations> + <citation type="bibtex">Credits : ABIMS team, Roscoff Marine Station</citation> + <citation type="bibtex">Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.</citation> + <citation type="bibtex">Version 1 : Scripts by Eric Fontanillas -- Galaxy integration by Julie Baffard</citation> + <citation type="bibtex">Version 2 : improvments by Victor Mataigne, Gildas le Corguillé, Misharl Monsoor</citation> + </citations> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01_phylip2fasta.py Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,59 @@ +#!/usr/bin/python + +## AUTHOR: Eric Fontanillas +## LAST VERSION: 20/08/14 by Julie BAFFARD + +## DESCRIPTION: formatting a fasta format into phylip format for using with PAML + +import string, os, sys +""" +if len(sys.argv) == 1: + print "put arguments!!" + print "USAGE: S01_phylip2fasta.py INPUT OUTPUT" +""" + +## INPUT +if os.path.isfile(sys.argv[1]) : + f1 = sys.argv[1] +else: + print "No existing phylip file ; exiting ..." + exit() + +F1 = open("%s" %f1, 'r') + +## OUTPUT +f2 = sys.argv[2] +F2 = open("%s" %f2, 'w') + +###### def1 ###### +# Dans un multialignement fasta, cette fonction permet de formatter les noms de chaque sequence fasta + +def format(File_IN): + c = 0 + fichier = "" + while 1 : + c = c + 1 + next = File_IN.readline() + if not next : + break + + S1 = string.split(next, "\t") # list : [name, sequence] --- BUG CORRECTED : "\t" instead of " " + fasta_name = S1[0] # get sequence name + fasta_seq = S1[1][:-1] # get sequence without the terminal '\n' + fichier = fichier + ">" + fasta_name + "\n" + fasta_seq + "\n" + + return (fichier,c) +#-#-#-#-#-#-#-#-#-#-# + +################### +### RUN RUN RUN ### +################### + +F1.readline() ## jump the first line + +fichier_txt, c = format(F1) ### DEF1 ### + +F2.write(fichier_txt) + +F1.close() +F2.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus10_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap2_1/1_1.000_160 +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>Pf5_1/1_1.000_160 +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus1_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ac7_1/1_1.000_160 +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>Am3_1/1_1.000_160 +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus1_sp3.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,6 @@ +>Ac5_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Am1_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Pf7_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus2_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ac6_1/1_1.000_160 +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA +>Am2_1/1_1.000_160 +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus3_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ac23_1/1_1.000_366 +ACTGAGGCTCGAACACAACAAAAAGGTGATGAGCAGTCAGCACTTAATAGAATATTACAGCAAGTAGCCAGTAATGTAGTTGATGTAGCAGCATTAGATAATCAAGGAGTAGACCAAGTTGAATACACAGATAGAGCTAGACAATACAGCCATAACCTGTCATCGTGGTGTGCTAGCACCCAGAAAGTACGAGGACCTCAACGTCTACCTGTTGGCGTAGCCACTCCACACACAGTCCTGTCTGGACAACCTATCACCTTAGCTGATATTGAACTGATAACTCATGCTGCCCAACAAGCGGCACGGTCACTACAAGAGGTCAAAGTTCGCCACAAAGAAGACTTGGTTGTACCTTTTGGCGTGCCA +>Ap46_1/1_1.000_217 +CCACAACCAAGTGGCGGGTATAACAGCACCGAGGCTCGAACACAGCAAAAAGGTGATGAGCAGTCAGCTCTTAATAGAATATTACAGCAAGTAGCCAGTAATGTAGTTGATGTAGCAGCATTAGATAATCAAGGAGTAGATCAAGTTGAGTACACAGATAGAGCTAGACAGTACAGCCATAACCTGTCATCATGGTGTGCTACCACCCAGAAAGTAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus4_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ac8_1/1_1.000_160 +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>Pf8_1/1_1.000_160 +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus5_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Am8_1/1_1.000_160 +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAAAGAGCTTCTATGGTT +>Pf9_1/1_1.000_160 +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAGGTAATTTCCCGATTA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus6_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap3_1/1_1.000_160 +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA +>Pf6_1/1_1.000_160 +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus7_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap1_1/1_1.000_160 +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>Pf4_1/1_1.000_160 +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus8_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap130_1/1_1.000_300 +CCAGTTCTAGGGTCTCAGTTTGGCTGTGTGTGTGTGTTAGGGTGTACCTCTGGGTGTTTGTGTATTTACATTCTGCTTCAGAGGACCGTGTGTATGCAGGTTAAGGTCGGCATCCGAGTGTTTATGCACACGGGCTTAGGTCTGTGTATGCATGATGTTTGTAGGAGAAGGCGAATGCGACATGTTGGCCAATGTGTTGAGGGTAAAGCTGCCCTCTGGGATAAAGCTGTCCATTATACTGTGTTATTGTTTGTTTTTTTAGATGTATTCTTTGATTCTTGTTATCACTTAGTTGTAGCG +>Pf172_1/1_1.000_246 +CACACACTGACAATAATATATACACACACGCACCCTCATATATTCACACACGCGTACACACATACACACACACGCGTACACGCGTTCACAGATACATATAGGCGTACATACATACATTCGTACACAAACGTATGCATACATACGCAAACAAACGTAAATACACACATGCGCAAATACACACCCACAGACAATCACACAGACAAATACACAGCTTTGACATTCAACCTTTCCTGTCCTGTTTTACGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/locus9_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap4_1/1_1.000_160 +CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA +>Pf10_1/1_1.000_160 +CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus10_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap21/11000160 +atactcaggcacacagcatttgtcgtactaggcgagagagagagaggaacgactaattgcaaccacgattacgttacatttgtttacaaaccaaacgtactggcgtcgaagataattaagaggaagctgactgaatgcgattggcgttggtctacgggtt +>Pf51/11000160 +atactcaggcacacagcatttgtcgtactaggcgagagagagagaggaacgactaattgcaaccacgattacgttacatttgtttacaaaccaaacgtactggcgtcgaagataattaagaggaagctgactgaatgcgattggcgttggtctacgggtt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus10_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Pf51/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=160; +format gap=- datatype=DNA; +matrix +Ap21/11000160 atactcaggcacacagcatttgtcgtactaggcgagagagagagaggaacgactaattgcaaccacgattacgttacatttgtttacaaaccaaacgtactggcgtcgaagataattaagaggaagctgactgaatgcgattggcgttggtctacgggtt +Pf51/11000160 atactcaggcacacagcatttgtcgtactaggcgagagagagagaggaacgactaattgcaaccacgattacgttacatttgtttacaaaccaaacgtactggcgtcgaagataattaagaggaagctgactgaatgcgattggcgttggtctacgggtt +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus10_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 160 +Ap21/11000160 atactcaggcacacagcatttgtcgtactaggcgagagagagagaggaacgactaattgcaaccacgattacgttacatttgtttacaaaccaaacgtactggcgtcgaagataattaagaggaagctgactgaatgcgattggcgttggtctacgggtt +Pf51/11000160 atactcaggcacacagcatttgtcgtactaggcgagagagagagaggaacgactaattgcaaccacgattacgttacatttgtttacaaaccaaacgtactggcgtcgaagataattaagaggaagctgactgaatgcgattggcgttggtctacgggtt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus1_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ac71/11000160 +gcacctagaattacccgaagttgcttggcaatagcgacacctaacggtcgccatgatatttgcaggaagaaggcatgtggtaccattgggaaccgtcaagcgtttcctcagccctgtggcagctgcccgtctgcgcccgtgtttgaccttgagcaccaag +>Am31/11000160 +gcacctagaattacccgaagttgcttggcaatagcgacacctaacggtcgccatgatatttgcaggaagaaggcatgtggtaccattgggaaccgtcaagcgtttcctcagccctgtggcagctgcccgtctgcgcccgtgtttgaccttgagcaccaag
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus1_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Am31/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=160; +format gap=- datatype=DNA; +matrix +Ac71/11000160 gcacctagaattacccgaagttgcttggcaatagcgacacctaacggtcgccatgatatttgcaggaagaaggcatgtggtaccattgggaaccgtcaagcgtttcctcagccctgtggcagctgcccgtctgcgcccgtgtttgaccttgagcaccaag +Am31/11000160 gcacctagaattacccgaagttgcttggcaatagcgacacctaacggtcgccatgatatttgcaggaagaaggcatgtggtaccattgggaaccgtcaagcgtttcctcagccctgtggcagctgcccgtctgcgcccgtgtttgaccttgagcaccaag +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus1_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 160 +Ac71/11000160 gcacctagaattacccgaagttgcttggcaatagcgacacctaacggtcgccatgatatttgcaggaagaaggcatgtggtaccattgggaaccgtcaagcgtttcctcagccctgtggcagctgcccgtctgcgcccgtgtttgaccttgagcaccaag +Am31/11000160 gcacctagaattacccgaagttgcttggcaatagcgacacctaacggtcgccatgatatttgcaggaagaaggcatgtggtaccattgggaaccgtcaagcgtttcctcagccctgtggcagctgcccgtctgcgcccgtgtttgaccttgagcaccaag
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus1_sp3.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,6 @@ +>Ac51/11000160 +gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt +>Am11/11000160 +gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt +>Pf71/11000160 +gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus1_sp3.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,11 @@ +#NEXUS +[Aligned to seq Pf71/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=3 nchar=160; +format gap=- datatype=DNA; +matrix +Ac51/11000160 gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt +Am11/11000160 gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt +Pf71/11000160 gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus1_sp3.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +3 160 +Ac51/11000160 gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt +Am11/11000160 gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt +Pf71/11000160 gcaccgggatgcggatttgctgacgatatggcaaaagcattgtcagcgtgcggaacctgtttatgtcacaccactggcatcttcctggccgtcgcagccttcgttctgacggcactcggtattgtctgcgtcacgcgatcagctgacccgagcctttggt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus2_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ac61/11000160 +cagcctaccactgagaagagatacttcaacatgtcttactggggtagaagtggtggtcgtacagcgggtggtaatgcaggacgtggtcgtggcggcggcagcggcagtggcagtagtcaaagtggtggtggcagctttctacaggaacgtatcaaagaga +>Am21/11000160 +cagcctaccactgagaagagatacttcaacatgtcttactggggtagaagtggtggtcgtacagcgggtggtaatgcaggacgtggtcgtggcggcggcagcggcagtggcagtagtcaaagtggtggtggcagctttctacaggaacgtatcaaagaga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus2_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Am21/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=160; +format gap=- datatype=DNA; +matrix +Ac61/11000160 cagcctaccactgagaagagatacttcaacatgtcttactggggtagaagtggtggtcgtacagcgggtggtaatgcaggacgtggtcgtggcggcggcagcggcagtggcagtagtcaaagtggtggtggcagctttctacaggaacgtatcaaagaga +Am21/11000160 cagcctaccactgagaagagatacttcaacatgtcttactggggtagaagtggtggtcgtacagcgggtggtaatgcaggacgtggtcgtggcggcggcagcggcagtggcagtagtcaaagtggtggtggcagctttctacaggaacgtatcaaagaga +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus2_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 160 +Ac61/11000160 cagcctaccactgagaagagatacttcaacatgtcttactggggtagaagtggtggtcgtacagcgggtggtaatgcaggacgtggtcgtggcggcggcagcggcagtggcagtagtcaaagtggtggtggcagctttctacaggaacgtatcaaagaga +Am21/11000160 cagcctaccactgagaagagatacttcaacatgtcttactggggtagaagtggtggtcgtacagcgggtggtaatgcaggacgtggtcgtggcggcggcagcggcagtggcagtagtcaaagtggtggtggcagctttctacaggaacgtatcaaagaga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus3_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ac231/11000366 +actgaggctcgaacacaacaaaaaggtgatgagcagtcagcacttaatagaatattacagcaagtagccagtaatgtagttgatgtagcagcattagataatcaaggagtagaccaagttgaatacacagatagagctagacaatacagccataacctgtcatcgtggtgtgctagcacccagaaagtacgaggacctcaacgtctacctgttggcgtagccactccacacacagtcctg +>Ap461/11000217 +---gaggctcgaacacagcaaaaaggtgatgagcagtcagctcttaatagaatattacagcaagtagccagtaatgtagttgatgtagcagcattagataatcaaggagtagatcaagttgagtacacagatagagctagacagtacagccataacctgtcatcatggtgtgctaccacccagaaagtac--------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus3_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Ac231/11000366 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=240; +format gap=- datatype=DNA; +matrix +Ac231/11000366 actgaggctcgaacacaacaaaaaggtgatgagcagtcagcacttaatagaatattacagcaagtagccagtaatgtagttgatgtagcagcattagataatcaaggagtagaccaagttgaatacacagatagagctagacaatacagccataacctgtcatcgtggtgtgctagcacccagaaagtacgaggacctcaacgtctacctgttggcgtagccactccacacacagtcctg +Ap461/11000217 ---gaggctcgaacacagcaaaaaggtgatgagcagtcagctcttaatagaatattacagcaagtagccagtaatgtagttgatgtagcagcattagataatcaaggagtagatcaagttgagtacacagatagagctagacagtacagccataacctgtcatcatggtgtgctaccacccagaaagtac-------------------------------------------------- +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus3_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 240 +Ac231/11000366 actgaggctcgaacacaacaaaaaggtgatgagcagtcagcacttaatagaatattacagcaagtagccagtaatgtagttgatgtagcagcattagataatcaaggagtagaccaagttgaatacacagatagagctagacaatacagccataacctgtcatcgtggtgtgctagcacccagaaagtacgaggacctcaacgtctacctgttggcgtagccactccacacacagtcctg +Ap461/11000217 ---gaggctcgaacacagcaaaaaggtgatgagcagtcagctcttaatagaatattacagcaagtagccagtaatgtagttgatgtagcagcattagataatcaaggagtagatcaagttgagtacacagatagagctagacagtacagccataacctgtcatcatggtgtgctaccacccagaaagtac--------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus4_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ac81/11000160 +atcaaagaagagcaacatcgagctactggcactggcaatggaatcctaattatagcagaaacaagcactggttgcctgttgtctgggtcagcaattggtagtagaggtgttcctgctgaagaagttggggtcaaagcaggacagatgcttttggataact +>Pf81/11000160 +atcaaagaagagcaacatcgagctactggcactggcaatggaatcctaattatagcagaaacaagcactggttgcctgttgtctgggtcagcaattggtagtagaggtgttcctgctgaagaagttggggtcaaagcaggacagatgcttttggataact
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus4_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Pf81/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=160; +format gap=- datatype=DNA; +matrix +Ac81/11000160 atcaaagaagagcaacatcgagctactggcactggcaatggaatcctaattatagcagaaacaagcactggttgcctgttgtctgggtcagcaattggtagtagaggtgttcctgctgaagaagttggggtcaaagcaggacagatgcttttggataact +Pf81/11000160 atcaaagaagagcaacatcgagctactggcactggcaatggaatcctaattatagcagaaacaagcactggttgcctgttgtctgggtcagcaattggtagtagaggtgttcctgctgaagaagttggggtcaaagcaggacagatgcttttggataact +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus4_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 160 +Ac81/11000160 atcaaagaagagcaacatcgagctactggcactggcaatggaatcctaattatagcagaaacaagcactggttgcctgttgtctgggtcagcaattggtagtagaggtgttcctgctgaagaagttggggtcaaagcaggacagatgcttttggataact +Pf81/11000160 atcaaagaagagcaacatcgagctactggcactggcaatggaatcctaattatagcagaaacaagcactggttgcctgttgtctgggtcagcaattggtagtagaggtgttcctgctgaagaagttggggtcaaagcaggacagatgcttttggataact
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus5_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Pf91/11000160 +gtattaataaaaggacaagactattatttaataccaagaaatctggccttaataagcatggttgcttatatcataagcatggtaaatcacattgtgttttccatgtgtttacccatcagatgtaaaaatattctgcatgaaataggtaatttcccgatta +>Am81/11000160 +gtattaataaaaggacaagactattatttaataccaagaaatctggccttaataagcatggttgcttatatcataagcatggtaaatcacattgtgttttccatgtgtttacccatcagatgtaaaaatattctgcatgaaata----------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus5_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Pf91/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=160; +format gap=- datatype=DNA; +matrix +Pf91/11000160 gtattaataaaaggacaagactattatttaataccaagaaatctggccttaataagcatggttgcttatatcataagcatggtaaatcacattgtgttttccatgtgtttacccatcagatgtaaaaatattctgcatgaaataggtaatttcccgatta +Am81/11000160 gtattaataaaaggacaagactattatttaataccaagaaatctggccttaataagcatggttgcttatatcataagcatggtaaatcacattgtgttttccatgtgtttacccatcagatgtaaaaatattctgcatgaaata---------------- +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus5_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 160 +Pf91/11000160 gtattaataaaaggacaagactattatttaataccaagaaatctggccttaataagcatggttgcttatatcataagcatggtaaatcacattgtgttttccatgtgtttacccatcagatgtaaaaatattctgcatgaaataggtaatttcccgatta +Am81/11000160 gtattaataaaaggacaagactattatttaataccaagaaatctggccttaataagcatggttgcttatatcataagcatggtaaatcacattgtgttttccatgtgtttacccatcagatgtaaaaatattctgcatgaaata----------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus6_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap31/11000160 +gccatgcagtacactggacttctgttattctgtttgtttgccttgacggcagccaaacccgcggaagaccttcaaatgctcatccgagccctgctccatgaaatagaagaggaaggtgaactccaagagcgaggcattggcgccgtgaagtatggtggaa +>Pf61/11000160 +gccatgcagtacactggacttctgttattctgtttgtttgccttgacggcagccaaacccgcggaagaccttcaaatgctcatccgagccctgctccatgaaatagaagaggaaggtgaactccaagagcgaggcattggcgccgtgaagtatggtggaa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus6_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Pf61/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=160; +format gap=- datatype=DNA; +matrix +Ap31/11000160 gccatgcagtacactggacttctgttattctgtttgtttgccttgacggcagccaaacccgcggaagaccttcaaatgctcatccgagccctgctccatgaaatagaagaggaaggtgaactccaagagcgaggcattggcgccgtgaagtatggtggaa +Pf61/11000160 gccatgcagtacactggacttctgttattctgtttgtttgccttgacggcagccaaacccgcggaagaccttcaaatgctcatccgagccctgctccatgaaatagaagaggaaggtgaactccaagagcgaggcattggcgccgtgaagtatggtggaa +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus6_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 160 +Ap31/11000160 gccatgcagtacactggacttctgttattctgtttgtttgccttgacggcagccaaacccgcggaagaccttcaaatgctcatccgagccctgctccatgaaatagaagaggaaggtgaactccaagagcgaggcattggcgccgtgaagtatggtggaa +Pf61/11000160 gccatgcagtacactggacttctgttattctgtttgtttgccttgacggcagccaaacccgcggaagaccttcaaatgctcatccgagccctgctccatgaaatagaagaggaaggtgaactccaagagcgaggcattggcgccgtgaagtatggtggaa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus7_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap11/11000160 +ggtcgccttataaaaaccaatccgaaacagttttcctttgaaacgtgccaaaaaccaaaaacatacttcaaatcttccagtgtctgttataaaggggtgagcgtagagagggcacttgtgagattggtgtctgggttaaagattttgccaaaaagcgatt +>Pf41/11000160 +ggtcgccttataaaaaccaatccgaaacagttttcctttgaaacgtgccaaaaaccaaaaacatacttcaaatcttccagtgtctgttataaaggggtgagcgtagagagggcacttgtgagattggtgtctgggttaaagattttgccaaaaagcgatt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus7_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Pf41/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=160; +format gap=- datatype=DNA; +matrix +Ap11/11000160 ggtcgccttataaaaaccaatccgaaacagttttcctttgaaacgtgccaaaaaccaaaaacatacttcaaatcttccagtgtctgttataaaggggtgagcgtagagagggcacttgtgagattggtgtctgggttaaagattttgccaaaaagcgatt +Pf41/11000160 ggtcgccttataaaaaccaatccgaaacagttttcctttgaaacgtgccaaaaaccaaaaacatacttcaaatcttccagtgtctgttataaaggggtgagcgtagagagggcacttgtgagattggtgtctgggttaaagattttgccaaaaagcgatt +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus7_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 160 +Ap11/11000160 ggtcgccttataaaaaccaatccgaaacagttttcctttgaaacgtgccaaaaaccaaaaacatacttcaaatcttccagtgtctgttataaaggggtgagcgtagagagggcacttgtgagattggtgtctgggttaaagattttgccaaaaagcgatt +Pf41/11000160 ggtcgccttataaaaaccaatccgaaacagttttcctttgaaacgtgccaaaaaccaaaaacatacttcaaatcttccagtgtctgttataaaggggtgagcgtagagagggcacttgtgagattggtgtctgggttaaagattttgccaaaaagcgatt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus9_sp2.fasta Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,4 @@ +>Ap41/11000160 +cggccgcggcgcgtcgttctcagccaagctgacttcgacttgagccgtccattcgcttatttacacgacgactgctcgaccctttacgacttagtcacacttccgtttaaccaggccctgctaccctccaatctcgtccaatcggtctctacgcatccga +>Pf101/11000160 +cggccgcggcgcgtcgttctcagccaagctgacttcgacttgagccgtccattcgcttatttacacgacgactgctcgaccctttacgacttagtcacacttccgtttaaccaggccctgctaccctccaatctcgtccaatcggtctctacgcatccga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus9_sp2.nxs Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,10 @@ +#NEXUS +[Aligned to seq Pf101/11000160 by BlastAlign. We have excluded sequences with more than 95% gaps] +BEGIN DATA; +dimensions ntax=2 nchar=160; +format gap=- datatype=DNA; +matrix +Ap41/11000160 cggccgcggcgcgtcgttctcagccaagctgacttcgacttgagccgtccattcgcttatttacacgacgactgctcgaccctttacgacttagtcacacttccgtttaaccaggccctgctaccctccaatctcgtccaatcggtctctacgcatccga +Pf101/11000160 cggccgcggcgcgtcgttctcagccaagctgacttcgacttgagccgtccattcgcttatttacacgacgactgctcgaccctttacgacttagtcacacttccgtttaaccaggccctgctaccctccaatctcgtccaatcggtctctacgcatccga +; +end; \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/locus9_sp2.phy Fri Feb 01 10:25:52 2019 -0500 @@ -0,0 +1,3 @@ +2 160 +Ap41/11000160 cggccgcggcgcgtcgttctcagccaagctgacttcgacttgagccgtccattcgcttatttacacgacgactgctcgaccctttacgacttagtcacacttccgtttaaccaggccctgctaccctccaatctcgtccaatcggtctctacgcatccga +Pf101/11000160 cggccgcggcgcgtcgttctcagccaagctgacttcgacttgagccgtccattcgcttatttacacgacgactgctcgaccctttacgacttagtcacacttccgtttaaccaggccctgctaccctccaatctcgtccaatcggtctctacgcatccga