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 NTHREADS 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 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).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible
to all nodes in the cluster.
--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 : Threads, 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.
