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author florianbegusch
date Thu, 03 Sep 2020 09:56:05 +0000
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<?xml version="1.0" ?>
<tool id="qiime_phylogeny_align-to-tree-mafft-iqtree" name="qiime phylogeny align-to-tree-mafft-iqtree"
      version="2020.8">
  <description>Build a phylogenetic tree using iqtree and mafft alignment.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime phylogeny align-to-tree-mafft-iqtree

--i-sequences=$isequences

#if str($pnthreads) != 'None':
--p-n-threads=$pnthreads
#end if

--p-mask-max-gap-frequency=$pmaskmaxgapfrequency

--p-mask-min-conservation=$pmaskminconservation

#if str($psubstitutionmodel) != 'None':
--p-substitution-model=$psubstitutionmodel
#end if

#if $pfast:
 --p-fast
#end if

#if str($palrt):
  --p-alrt=$palrt
#end if
#if str($pseed):
  --p-seed=$pseed
#end if
#if str($pstopiter):
  --p-stop-iter=$pstopiter
#end if
#if str($pperturbnnistrength):
  --p-perturb-nni-strength=$pperturbnnistrength
#end if
--o-alignment=oalignment

--o-masked-alignment=omaskedalignment

--o-tree=otree

--o-rooted-tree=orootedtree

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp orootedtree.qza $orootedtree

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a iqtree based rooted phylogenetic tree.           [required]" name="isequences" optional="False" type="data" />
    <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Int % Range(1">Int % Range(1</option>
      <option value="None">None</option>
    </param>
    <param exclude_max="False" label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns  regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" max="1" min="0" name="pmaskmaxgapfrequency" optional="True" type="float" value="1.0" />
    <param exclude_max="False" label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of  0.4 is provided, a column will only be retained  if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" max="1" min="0" name="pmaskminconservation" optional="True" type="float" value="0.4" />
    <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="JC">JC</option>
      <option value="JC+I">JC+I</option>
      <option value="JC+G">JC+G</option>
      <option value="JC+I+G">JC+I+G</option>
      <option value="JC+R2">JC+R2</option>
      <option value="JC+R3">JC+R3</option>
      <option value="JC+R4">JC+R4</option>
      <option value="JC+R5">JC+R5</option>
      <option value="JC+R6">JC+R6</option>
      <option value="JC+R7">JC+R7</option>
      <option value="JC+R8">JC+R8</option>
      <option value="JC+R9">JC+R9</option>
      <option value="JC+R10">JC+R10</option>
      <option value="F81">F81</option>
      <option value="F81+I">F81+I</option>
      <option value="F81+G">F81+G</option>
      <option value="F81+I+G">F81+I+G</option>
      <option value="F81+R2">F81+R2</option>
      <option value="F81+R3">F81+R3</option>
      <option value="F81+R4">F81+R4</option>
      <option value="F81+R5">F81+R5</option>
      <option value="F81+R6">F81+R6</option>
      <option value="F81+R7">F81+R7</option>
      <option value="F81+R8">F81+R8</option>
      <option value="F81+R9">F81+R9</option>
      <option value="F81+R10">F81+R10</option>
      <option value="K80">K80</option>
      <option value="K80+I">K80+I</option>
      <option value="K80+G">K80+G</option>
      <option value="K80+I+G">K80+I+G</option>
      <option value="K80+R2">K80+R2</option>
      <option value="K80+R3">K80+R3</option>
      <option value="K80+R4">K80+R4</option>
      <option value="K80+R5">K80+R5</option>
      <option value="K80+R6">K80+R6</option>
      <option value="K80+R7">K80+R7</option>
      <option value="K80+R8">K80+R8</option>
      <option value="K80+R9">K80+R9</option>
      <option value="K80+R10">K80+R10</option>
      <option value="HKY">HKY</option>
      <option value="HKY+I">HKY+I</option>
      <option value="HKY+G">HKY+G</option>
      <option value="HKY+I+G">HKY+I+G</option>
      <option value="HKY+R2">HKY+R2</option>
      <option value="HKY+R3">HKY+R3</option>
      <option value="HKY+R4">HKY+R4</option>
      <option value="HKY+R5">HKY+R5</option>
      <option value="HKY+R6">HKY+R6</option>
      <option value="HKY+R7">HKY+R7</option>
      <option value="HKY+R8">HKY+R8</option>
      <option value="HKY+R9">HKY+R9</option>
      <option value="HKY+R10">HKY+R10</option>
      <option value="TNe">TNe</option>
      <option value="TNe+I">TNe+I</option>
      <option value="TNe+G">TNe+G</option>
      <option value="TNe+I+G">TNe+I+G</option>
      <option value="TNe+R2">TNe+R2</option>
      <option value="TNe+R3">TNe+R3</option>
      <option value="TNe+R4">TNe+R4</option>
      <option value="TNe+R5">TNe+R5</option>
      <option value="TNe+R6">TNe+R6</option>
      <option value="TNe+R7">TNe+R7</option>
      <option value="TNe+R8">TNe+R8</option>
      <option value="TNe+R9">TNe+R9</option>
      <option value="TNe+R10">TNe+R10</option>
      <option value="TN">TN</option>
      <option value="TN+I">TN+I</option>
      <option value="TN+G">TN+G</option>
      <option value="TN+I+G">TN+I+G</option>
      <option value="TN+R2">TN+R2</option>
      <option value="TN+R3">TN+R3</option>
      <option value="TN+R4">TN+R4</option>
      <option value="TN+R5">TN+R5</option>
      <option value="TN+R6">TN+R6</option>
      <option value="TN+R7">TN+R7</option>
      <option value="TN+R8">TN+R8</option>
      <option value="TN+R9">TN+R9</option>
      <option value="TN+R10">TN+R10</option>
      <option value="K81">K81</option>
      <option value="K81+I">K81+I</option>
      <option value="K81+G">K81+G</option>
      <option value="K81+I+G">K81+I+G</option>
      <option value="K81+R2">K81+R2</option>
      <option value="K81+R3">K81+R3</option>
      <option value="K81+R4">K81+R4</option>
      <option value="K81+R5">K81+R5</option>
      <option value="K81+R6">K81+R6</option>
      <option value="K81+R7">K81+R7</option>
      <option value="K81+R8">K81+R8</option>
      <option value="K81+R9">K81+R9</option>
      <option value="K81+R10">K81+R10</option>
      <option value="K81u">K81u</option>
      <option value="K81u+I">K81u+I</option>
      <option value="K81u+G">K81u+G</option>
      <option value="K81u+I+G">K81u+I+G</option>
      <option value="K81u+R2">K81u+R2</option>
      <option value="K81u+R3">K81u+R3</option>
      <option value="K81u+R4">K81u+R4</option>
      <option value="K81u+R5">K81u+R5</option>
      <option value="K81u+R6">K81u+R6</option>
      <option value="K81u+R7">K81u+R7</option>
      <option value="K81u+R8">K81u+R8</option>
      <option value="K81u+R9">K81u+R9</option>
      <option value="K81u+R10">K81u+R10</option>
      <option value="TPM2">TPM2</option>
      <option value="TPM2+I">TPM2+I</option>
      <option value="TPM2+G">TPM2+G</option>
      <option value="TPM2+I+G">TPM2+I+G</option>
      <option value="TPM2+R2">TPM2+R2</option>
      <option value="TPM2+R3">TPM2+R3</option>
      <option value="TPM2+R4">TPM2+R4</option>
      <option value="TPM2+R5">TPM2+R5</option>
      <option value="TPM2+R6">TPM2+R6</option>
      <option value="TPM2+R7">TPM2+R7</option>
      <option value="TPM2+R8">TPM2+R8</option>
      <option value="TPM2+R9">TPM2+R9</option>
      <option value="TPM2+R10">TPM2+R10</option>
      <option value="TPM2u">TPM2u</option>
      <option value="TPM2u+I">TPM2u+I</option>
      <option value="TPM2u+G">TPM2u+G</option>
      <option value="TPM2u+I+G">TPM2u+I+G</option>
      <option value="TPM2u+R2">TPM2u+R2</option>
      <option value="TPM2u+R3">TPM2u+R3</option>
      <option value="TPM2u+R4">TPM2u+R4</option>
      <option value="TPM2u+R5">TPM2u+R5</option>
      <option value="TPM2u+R6">TPM2u+R6</option>
      <option value="TPM2u+R7">TPM2u+R7</option>
      <option value="TPM2u+R8">TPM2u+R8</option>
      <option value="TPM2u+R9">TPM2u+R9</option>
      <option value="TPM2u+R10">TPM2u+R10</option>
      <option value="TPM3">TPM3</option>
      <option value="TPM3+I">TPM3+I</option>
      <option value="TPM3+G">TPM3+G</option>
      <option value="TPM3+I+G">TPM3+I+G</option>
      <option value="TPM3+R2">TPM3+R2</option>
      <option value="TPM3+R3">TPM3+R3</option>
      <option value="TPM3+R4">TPM3+R4</option>
      <option value="TPM3+R5">TPM3+R5</option>
      <option value="TPM3+R6">TPM3+R6</option>
      <option value="TPM3+R7">TPM3+R7</option>
      <option value="TPM3+R8">TPM3+R8</option>
      <option value="TPM3+R9">TPM3+R9</option>
      <option value="TPM3+R10">TPM3+R10</option>
      <option value="TPM3u">TPM3u</option>
      <option value="TPM3u+I">TPM3u+I</option>
      <option value="TPM3u+G">TPM3u+G</option>
      <option value="TPM3u+I+G">TPM3u+I+G</option>
      <option value="TPM3u+R2">TPM3u+R2</option>
      <option value="TPM3u+R3">TPM3u+R3</option>
      <option value="TPM3u+R4">TPM3u+R4</option>
      <option value="TPM3u+R5">TPM3u+R5</option>
      <option value="TPM3u+R6">TPM3u+R6</option>
      <option value="TPM3u+R7">TPM3u+R7</option>
      <option value="TPM3u+R8">TPM3u+R8</option>
      <option value="TPM3u+R9">TPM3u+R9</option>
      <option value="TPM3u+R10">TPM3u+R10</option>
      <option value="TIMe">TIMe</option>
      <option value="TIMe+I">TIMe+I</option>
      <option value="TIMe+G">TIMe+G</option>
      <option value="TIMe+I+G">TIMe+I+G</option>
      <option value="TIMe+R2">TIMe+R2</option>
      <option value="TIMe+R3">TIMe+R3</option>
      <option value="TIMe+R4">TIMe+R4</option>
      <option value="TIMe+R5">TIMe+R5</option>
      <option value="TIMe+R6">TIMe+R6</option>
      <option value="TIMe+R7">TIMe+R7</option>
      <option value="TIMe+R8">TIMe+R8</option>
      <option value="TIMe+R9">TIMe+R9</option>
      <option value="TIMe+R10">TIMe+R10</option>
      <option value="TIM">TIM</option>
      <option value="TIM+I">TIM+I</option>
      <option value="TIM+G">TIM+G</option>
      <option value="TIM+I+G">TIM+I+G</option>
      <option value="TIM+R2">TIM+R2</option>
      <option value="TIM+R3">TIM+R3</option>
      <option value="TIM+R4">TIM+R4</option>
      <option value="TIM+R5">TIM+R5</option>
      <option value="TIM+R6">TIM+R6</option>
      <option value="TIM+R7">TIM+R7</option>
      <option value="TIM+R8">TIM+R8</option>
      <option value="TIM+R9">TIM+R9</option>
      <option value="TIM+R10">TIM+R10</option>
      <option value="TIM2e">TIM2e</option>
      <option value="TIM2e+I">TIM2e+I</option>
      <option value="TIM2e+G">TIM2e+G</option>
      <option value="TIM2e+I+G">TIM2e+I+G</option>
      <option value="TIM2e+R2">TIM2e+R2</option>
      <option value="TIM2e+R3">TIM2e+R3</option>
      <option value="TIM2e+R4">TIM2e+R4</option>
      <option value="TIM2e+R5">TIM2e+R5</option>
      <option value="TIM2e+R6">TIM2e+R6</option>
      <option value="TIM2e+R7">TIM2e+R7</option>
      <option value="TIM2e+R8">TIM2e+R8</option>
      <option value="TIM2e+R9">TIM2e+R9</option>
      <option value="TIM2e+R10">TIM2e+R10</option>
      <option value="TIM2">TIM2</option>
      <option value="TIM2+I">TIM2+I</option>
      <option value="TIM2+G">TIM2+G</option>
      <option value="TIM2+I+G">TIM2+I+G</option>
      <option value="TIM2+R2">TIM2+R2</option>
      <option value="TIM2+R3">TIM2+R3</option>
      <option value="TIM2+R4">TIM2+R4</option>
      <option value="TIM2+R5">TIM2+R5</option>
      <option value="TIM2+R6">TIM2+R6</option>
      <option value="TIM2+R7">TIM2+R7</option>
      <option value="TIM2+R8">TIM2+R8</option>
      <option value="TIM2+R9">TIM2+R9</option>
      <option value="TIM2+R10">TIM2+R10</option>
      <option value="TIM3e">TIM3e</option>
      <option value="TIM3e+I">TIM3e+I</option>
      <option value="TIM3e+G">TIM3e+G</option>
      <option value="TIM3e+I+G">TIM3e+I+G</option>
      <option value="TIM3e+R2">TIM3e+R2</option>
      <option value="TIM3e+R3">TIM3e+R3</option>
      <option value="TIM3e+R4">TIM3e+R4</option>
      <option value="TIM3e+R5">TIM3e+R5</option>
      <option value="TIM3e+R6">TIM3e+R6</option>
      <option value="TIM3e+R7">TIM3e+R7</option>
      <option value="TIM3e+R8">TIM3e+R8</option>
      <option value="TIM3e+R9">TIM3e+R9</option>
      <option value="TIM3e+R10">TIM3e+R10</option>
      <option value="TIM3">TIM3</option>
      <option value="TIM3+I">TIM3+I</option>
      <option value="TIM3+G">TIM3+G</option>
      <option value="TIM3+I+G">TIM3+I+G</option>
      <option value="TIM3+R2">TIM3+R2</option>
      <option value="TIM3+R3">TIM3+R3</option>
      <option value="TIM3+R4">TIM3+R4</option>
      <option value="TIM3+R5">TIM3+R5</option>
      <option value="TIM3+R6">TIM3+R6</option>
      <option value="TIM3+R7">TIM3+R7</option>
      <option value="TIM3+R8">TIM3+R8</option>
      <option value="TIM3+R9">TIM3+R9</option>
      <option value="TIM3+R10">TIM3+R10</option>
      <option value="TVMe">TVMe</option>
      <option value="TVMe+I">TVMe+I</option>
      <option value="TVMe+G">TVMe+G</option>
      <option value="TVMe+I+G">TVMe+I+G</option>
      <option value="TVMe+R2">TVMe+R2</option>
      <option value="TVMe+R3">TVMe+R3</option>
      <option value="TVMe+R4">TVMe+R4</option>
      <option value="TVMe+R5">TVMe+R5</option>
      <option value="TVMe+R6">TVMe+R6</option>
      <option value="TVMe+R7">TVMe+R7</option>
      <option value="TVMe+R8">TVMe+R8</option>
      <option value="TVMe+R9">TVMe+R9</option>
      <option value="TVMe+R10">TVMe+R10</option>
      <option value="TVM">TVM</option>
      <option value="TVM+I">TVM+I</option>
      <option value="TVM+G">TVM+G</option>
      <option value="TVM+I+G">TVM+I+G</option>
      <option value="TVM+R2">TVM+R2</option>
      <option value="TVM+R3">TVM+R3</option>
      <option value="TVM+R4">TVM+R4</option>
      <option value="TVM+R5">TVM+R5</option>
      <option value="TVM+R6">TVM+R6</option>
      <option value="TVM+R7">TVM+R7</option>
      <option value="TVM+R8">TVM+R8</option>
      <option value="TVM+R9">TVM+R9</option>
      <option value="TVM+R10">TVM+R10</option>
      <option value="SYM">SYM</option>
      <option value="SYM+I">SYM+I</option>
      <option value="SYM+G">SYM+G</option>
      <option value="SYM+I+G">SYM+I+G</option>
      <option value="SYM+R2">SYM+R2</option>
      <option value="SYM+R3">SYM+R3</option>
      <option value="SYM+R4">SYM+R4</option>
      <option value="SYM+R5">SYM+R5</option>
      <option value="SYM+R6">SYM+R6</option>
      <option value="SYM+R7">SYM+R7</option>
      <option value="SYM+R8">SYM+R8</option>
      <option value="SYM+R9">SYM+R9</option>
      <option value="SYM+R10">SYM+R10</option>
      <option value="GTR">GTR</option>
      <option value="GTR+I">GTR+I</option>
      <option value="GTR+G">GTR+G</option>
      <option value="GTR+I+G">GTR+I+G</option>
      <option value="GTR+R2">GTR+R2</option>
      <option value="GTR+R3">GTR+R3</option>
      <option value="GTR+R4">GTR+R4</option>
      <option value="GTR+R5">GTR+R5</option>
      <option value="GTR+R6">GTR+R6</option>
      <option value="GTR+R7">GTR+R7</option>
      <option value="GTR+R8">GTR+R8</option>
      <option value="GTR+R9">GTR+R9</option>
      <option value="GTR+R10">GTR+R10</option>
      <option value="MFP">MFP</option>
      <option value="TEST">TEST</option>
    </param>
    <param label="--p-fast: --p-fast: / --p-no-fast  Fast search to resemble FastTree.   [default: False]" name="pfast" selected="False" type="boolean" />
    <param label="--p-alrt: INTEGER        Single branch test method. Number of bootstrap Range(1000, None)     replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended.                 [optional]" name="palrt" optional="False" type="text" />
    <param label="--p-seed: INTEGER        Random number seed for the iqtree parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen.                                   [optional]" name="pseed" optional="False" type="text" />
    <param label="--p-stop-iter: INTEGER   Number of unsuccessful iterations to stop. If not Range(1, None)        set, program defaults will be used. See IQ-TREE manual for details.                       [optional]" name="pstopiter" optional="False" type="text" />
    <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 1.0)      Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details.                       [optional]" name="pperturbnnistrength" optional="False" type="text" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
    <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
    <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
    <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
    
  </outputs>

  <help><![CDATA[
Build a phylogenetic tree using iqtree and mafft alignment.
###############################################################

This pipeline will start by creating a sequence alignment using MAFFT,
after which any alignment columns that are phylogenetically uninformative
or ambiguously aligned will be removed (masked). The resulting masked
alignment will be used to infer a phylogenetic tree using IQ-TREE. By
default the best fit substitution model will be determined by ModelFinder
prior to phylogenetic inference. The resulting tree will be subsequently
rooted at its midpoint. Output files from each step of the pipeline will be
saved. This includes both the unmasked and masked MAFFT alignment from
q2-alignment methods, and both the rooted and unrooted phylogenies from
q2-phylogeny methods.

Parameters
----------
sequences : FeatureData[Sequence]
    The sequences to be used for creating a iqtree based rooted
    phylogenetic tree.
n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of threads. (Use 0 to automatically use all available cores
    This value is used when aligning the sequences and creating the tree
    with iqtree.
mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
    The maximum relative frequency of gap characters in a column for the
    column to be retained. This relative frequency must be a number between
    0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
    gap characters, and 1.0 retains all columns  regardless of gap
    character frequency. This value is used when masking the aligned
    sequences.
mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
    The minimum relative frequency of at least one non-gap character in a
    column for that column to be retained. This relative frequency must be
    a number between 0.0 and 1.0 (inclusive). For example, if a value of
    0.4 is provided, a column will only be retained  if it contains at
    least one character that is present in at least 40% of the sequences.
    This value is used when masking the aligned sequences.
substitution_model : Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional
    Model of Nucleotide Substitution. If not provided, IQ-TREE will
    determine the best fit substitution model automatically.
fast : Bool, optional
    Fast search to resemble FastTree.
alrt : Int % Range(1000, None), optional
    Single branch test method. Number of bootstrap replicates to perform an
    SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
    replicates is recomended.
seed : Int, optional
    Random number seed for the iqtree parsimony starting tree. This allows
    you to reproduce tree results. If not supplied then one will be
    randomly chosen.
stop_iter : Int % Range(1, None), optional
    Number of unsuccessful iterations to stop. If not set, program defaults
    will be used. See IQ-TREE manual for details.
perturb_nni_strength : Float % Range(0.01, 1.0), optional
    Perturbation strength for randomized NNI. If not set, program defaults
    will be used. See IQ-TREE manual for details.

Returns
-------
alignment : FeatureData[AlignedSequence]
    The aligned sequences.
masked_alignment : FeatureData[AlignedSequence]
    The masked alignment.
tree : Phylogeny[Unrooted]
    The unrooted phylogenetic tree.
rooted_tree : Phylogeny[Rooted]
    The rooted phylogenetic tree.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>