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raxml-rapid-bootstrap: Construct a phylogenetic tree with bootstrap supports using RAxML.

Citations

Docstring:

Usage: qiime phylogeny raxml-rapid-bootstrap [OPTIONS]

  Construct a phylogenetic tree with RAxML with the addition of rapid
  bootstrapping support values. See:
  https://sco.h-its.org/exelixis/web/software/raxml/

Inputs:
  --i-alignment ARTIFACT FeatureData[AlignedSequence]
                          Aligned sequences to be used for phylogenetic
                          reconstruction.                           [required]
Parameters:
  --p-seed INTEGER        Random number seed for the parsimony starting tree.
                          This allows you to reproduce tree results. If not
                          supplied then one will be randomly chosen.
                                                                    [optional]
  --p-rapid-bootstrap-seed INTEGER
                          Specify a random seed for rapid bootstrapping. This
                          allows you to reproduce rapid bootstrap results. If
                          not supplied then one will be randomly chosen.
                                                                    [optional]
  --p-bootstrap-replicates INTEGER
    Range(10, None)       The number of bootstrap searches to perform.
                                                                [default: 100]
  --p-n-threads INTEGER   The number of threads to use for multithreaded
    Range(1, None)        processing. Using more than one thread will enable
                          the PTHREADS version of RAxML.          [default: 1]
  --p-raxml-version TEXT Choices('Standard', 'SSE3', 'AVX2')
                          Select a specific CPU optimization of RAxML to use.
                          The SSE3 versions will run approximately 40% faster
                          than the standard version. The AVX2 version will run
                          10-30% faster than the SSE3 version.
                                                         [default: 'Standard']
  --p-substitution-model TEXT Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT',
    'GTRCATI')            Model of Nucleotide Substitution
                                                         [default: 'GTRGAMMA']
Outputs:
  --o-tree ARTIFACT       The resulting phylogenetic tree.
    Phylogeny[Unrooted]                                             [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.phylogeny.methods import raxml_rapid_bootstrap

Docstring:

Construct a phylogenetic tree with bootstrap supports using RAxML.

Construct a phylogenetic tree with RAxML with the addition of rapid
bootstrapping support values. See:
https://sco.h-its.org/exelixis/web/software/raxml/

Parameters
----------
alignment : FeatureData[AlignedSequence]
    Aligned sequences to be used for phylogenetic reconstruction.
seed : Int, optional
    Random number seed for the parsimony starting tree. This allows you to
    reproduce tree results. If not supplied then one will be randomly
    chosen.
rapid_bootstrap_seed : Int, optional
    Specify a random seed for rapid bootstrapping. This allows you to
    reproduce rapid bootstrap results. If not supplied then one will be
    randomly chosen.
bootstrap_replicates : Int % Range(10, None), optional
    The number of bootstrap searches to perform.
n_threads : Int % Range(1, None), optional
    The number of threads to use for multithreaded processing. Using more
    than one thread will enable the PTHREADS version of RAxML.
raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
    Select a specific CPU optimization of RAxML to use. The SSE3 versions
    will run approximately 40% faster than the standard version. The AVX2
    version will run 10-30% faster than the SSE3 version.
substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
    Model of Nucleotide Substitution

Returns
-------
tree : Phylogeny[Unrooted]
    The resulting phylogenetic tree.