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

Citations

[phylogeny:raxml-rapid-bootstrap:Sta14]Alexandros Stamatakis. Raxml version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9):1312–1313, 2014. URL: http://dx.doi.org/10.1093/bioinformatics/btu033, doi:10.1093/bioinformatics/btu033.
[phylogeny:raxml-rapid-bootstrap:SHR08]Alexandros Stamatakis, Paul Hoover, and Jacques Rougemont. A rapid bootstrap algorithm for the raxml web servers. Systematic Biology, 57(5):758–771, 2008. URL: http://dx.doi.org/10.1080/10635150802429642, doi:10.1080/10635150802429642.

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/

Options:
  --i-alignment ARTIFACT PATH FeatureData[AlignedSequence]
                                  Aligned sequences to be used for
                                  phylogenetic reconstruction.  [required]
  --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
                                  The number of bootstrap searches to perform.
                                  [default: 100]
  --p-n-threads INTEGER RANGE     The number of threads to use for
                                  multithreaded processing. Using more than
                                  one thread will enable the PTHREADS version
                                  of RAxML.  [default: 1]
  --p-raxml-version [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 [GTRCAT|GTRGAMMA|GTRGAMMAI|GTRCATI]
                                  Model of Nucleotide Substitution  [default:
                                  GTRGAMMA]
  --o-tree ARTIFACT PATH Phylogeny[Unrooted]
                                  The resulting phylogenetic tree.  [required
                                  if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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({'AVX2', 'SSE3', 'Standard'}), 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({'GTRCAT', 'GTRCATI', 'GTRGAMMA', 'GTRGAMMAI'}), optional
    Model of Nucleotide Substitution

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