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