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author florianbegusch
date Fri, 04 Sep 2020 12:46:48 +0000
parents d93d8888f0b0
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<?xml version="1.0" ?>
<tool id="qiime_phylogeny_iqtree-ultrafast-bootstrap" name="qiime phylogeny iqtree-ultrafast-bootstrap"
      version="2020.8">
  <description>Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime phylogeny iqtree-ultrafast-bootstrap

--i-alignment=$ialignment

#if str($pseed):
  --p-seed=$pseed
#end if
#if str($pncores) != 'None':
--p-n-cores=$pncores
#end if

#set $pncoresmax = '${GALAXY_SLOTS:-4}'

#if str($pncoresmax):
  --p-n-cores-max=$pncoresmax
#end if

--p-n-runs=$pnruns

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

--p-bootstrap-replicates=$pbootstrapreplicates

#if str($pninitparstrees):
  --p-n-init-pars-trees=$pninitparstrees
#end if
#if str($pntopinittrees):
  --p-n-top-init-trees=$pntopinittrees
#end if
#if str($pnbestretaintrees):
  --p-n-best-retain-trees=$pnbestretaintrees
#end if
#if str($pstopiter):
  --p-stop-iter=$pstopiter
#end if
#if str($pperturbnnistrength):
  --p-perturb-nni-strength=$pperturbnnistrength
#end if
#if str($psprradius):
  --p-spr-radius=$psprradius
#end if
#if str($pnmaxufbootiter):
  --p-n-max-ufboot-iter=$pnmaxufbootiter
#end if
#if str($pnufbootsteps):
  --p-n-ufboot-steps=$pnufbootsteps
#end if
#if str($pmincorufboot):
  --p-min-cor-ufboot=$pmincorufboot
#end if
#if str($pepbreakufboot):
  --p-ep-break-ufboot=$pepbreakufboot
#end if
#if $pallnni:
 --p-allnni
#end if

#if str($palrt):
  --p-alrt=$palrt
#end if
#if $pabayes:
 --p-abayes
#end if

#if str($plbp):
  --p-lbp=$plbp
#end if
#if $pbnni:
 --p-bnni
#end if

#if $psafe:
 --p-safe
#end if

--o-tree=otree

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

;
cp otree.qza $otree

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data" />
    <param label="--p-seed: INTEGER        Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="False" type="text" />
    <param label="--p-n-cores: " name="pncores" 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 label="--p-n-runs: INTEGER      Number of indepedent runs. Multiple  independent Range(1, None)        runs (e.g. 10) can outperform a single run in terms of likelihood maximisation.             [default: 1]" min="1" name="pnruns" optional="True" type="integer" value="1" />
    <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-bootstrap-replicates: INTEGER Range(1000, None)     The number of bootstrap searches to perform. Minimum of 1000 recomended.          [default: 1000]" min="1000" name="pbootstrapreplicates" optional="True" type="integer" value="1000" />
    <param label="--p-n-init-pars-trees: INTEGER Range(1, None)        Number of initial parsimony trees. If not set, program defaults will be used. See IQ-TREE manual for details.                              [optional]" name="pninitparstrees" optional="False" type="text" />
    <param label="--p-n-top-init-trees: INTEGER Range(1, None)        Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details.                                  [optional]" name="pntopinittrees" optional="False" type="text" />
    <param label="--p-n-best-retain-trees: INTEGER Range(1, None)        Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details.                       [optional]" name="pnbestretaintrees" 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="--p-spr-radius: INTEGER  Radius for parsimony SPR search. If not set, Range(1, None)        program defaults will be used. See IQ-TREE manual for details.                              [optional]" name="psprradius" optional="False" type="text" />
    <param label="--p-n-max-ufboot-iter: INTEGER Range(1, None)        Maximum number of iterations. If not set, program defaults will be used. See IQ-TREE manual for details.                                  [optional]" name="pnmaxufbootiter" optional="False" type="text" />
    <param label="--p-n-ufboot-steps: INTEGER Range(1, None)        Number of iterations for UFBoot stopping rule. If not set, program defaults will be used.See IQ-TREE manual for details.                       [optional]" name="pnufbootsteps" optional="False" type="text" />
    <param label="--p-min-cor-ufboot: NUMBER Range(0.51, 0.99)     Minimum correlation coefficient. If not set, program defaults will be used.See IQ-TREE manual for details.                                  [optional]" name="pmincorufboot" optional="False" type="text" />
    <param label="--p-ep-break-ufboot: NUMBER Range(0.01, 0.99)     Epsilon value to break tie. If not set, program defaults will be used. See IQ-TREE manual for details.                                  [optional]" name="pepbreakufboot" optional="False" type="text" />
    <param label="--p-allnni: --p-allnni: / --p-no-allnni Perform more thorough NNI search.   [default: False]" name="pallnni" 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. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes.              [optional]" name="palrt" optional="False" type="text" />
    <param label="--p-abayes: --p-abayes: / --p-no-abayes Single branch test method. Performs an approximate Bayes test. Can be used with other \'single branch test methods\' and ultrafast bootstrap. Values reported in the order of: alrt, lbp, abayes, ufboot. [default: False]" name="pabayes" selected="False" type="boolean" />
    <param label="--p-lbp: INTEGER         Single branch test method. Number of bootstrap Range(1000, None)     replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes, ufboot.                [optional]" name="plbp" optional="False" type="text" />
    <param label="--p-bnni: --p-bnni: / --p-no-bnni  Optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations.            [default: False]" name="pbnni" selected="False" type="boolean" />
    <param label="--p-safe: --p-safe: / --p-no-safe  Safe likelihood kernel to avoid numerical underflow.                          [default: False]" name="psafe" selected="False" type="boolean" />
    <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}: tree.qza" name="otree" />
    
  </outputs>

  <help><![CDATA[
Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
###############################################################

Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
automatic model selection and bootstrap supports.

Parameters
----------
alignment : FeatureData[AlignedSequence]
    Aligned sequences to be used for phylogenetic reconstruction.
seed : Int, optional
    Random number seed. If not set, program defaults will be used. See IQ-
    TREE manual for details.
n_cores : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of cores to use for parallel processing. Use `auto` to let
    IQ-TREE automatically determine the optimal number of cores to use.
n_cores_max : Int % Range(2, None), optional
    Limits the maximum number of cores to be used when 'n_cores' is set to
    'auto'.
n_runs : Int % Range(1, None), optional
    Number of indepedent runs. Multiple  independent runs (e.g. 10) can
    outperform a single run in terms of likelihood maximisation.
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.
bootstrap_replicates : Int % Range(1000, None), optional
    The number of bootstrap searches to perform. Minimum of 1000
    recomended.
n_init_pars_trees : Int % Range(1, None), optional
    Number of initial parsimony trees. If not set, program defaults will be
    used. See IQ-TREE manual for details.
n_top_init_trees : Int % Range(1, None), optional
    Number of top initial trees. If not set, program defaults will be used.
    See IQ-TREE manual for details.
n_best_retain_trees : Int % Range(1, None), optional
    Number of best trees retained during search. If not set, program
    defaults will be used. See IQ-TREE manual for details.
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.
spr_radius : Int % Range(1, None), optional
    Radius for parsimony SPR search. If not set, program defaults will be
    used. See IQ-TREE manual for details.
n_max_ufboot_iter : Int % Range(1, None), optional
    Maximum number of iterations. If not set, program defaults will be
    used. See IQ-TREE manual for details.
n_ufboot_steps : Int % Range(1, None), optional
    Number of iterations for UFBoot stopping rule. If not set, program
    defaults will be used.See IQ-TREE manual for details.
min_cor_ufboot : Float % Range(0.51, 0.99), optional
    Minimum correlation coefficient. If not set, program defaults will be
    used.See IQ-TREE manual for details.
ep_break_ufboot : Float % Range(0.01, 0.99), optional
    Epsilon value to break tie. If not set, program defaults will be used.
    See IQ-TREE manual for details.
allnni : Bool, optional
    Perform more thorough NNI search.
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. Can be used with other 'single branch test
    methods'. Values reported in the order of: alrt, lbp, abayes.
abayes : Bool, optional
    Single branch test method. Performs an approximate Bayes test. Can be
    used with other 'single branch test methods' and ultrafast bootstrap.
    Values reported in the order of: alrt, lbp, abayes, ufboot.
lbp : Int % Range(1000, None), optional
    Single branch test method. Number of bootstrap replicates to perform a
    fast local bootstrap probability method. Minimum of 1000 replicates is
    recomended. Can be used with other 'single branch test methods'. Values
    reported in the order of: alrt, lbp, abayes, ufboot.
bnni : Bool, optional
    Optimize UFBoot trees by NNI on bootstrap alignment. This option
    reduces the risk of overestimating branch supports with UFBoot due to
    severe model violations.
safe : Bool, optional
    Safe likelihood kernel to avoid numerical underflow.

Returns
-------
tree : Phylogeny[Unrooted]
    The resulting phylogenetic tree.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>