raxml: Construct a phylogenetic tree with RAxML.¶

Docstring:

Usage: qiime phylogeny raxml [OPTIONS]

  Construct a phylogenetic tree with RAxML. 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-n-searches INTEGER  The number of independent maximum likelihood
    Range(1, None)        searches to perform. The single best scoring tree is
                          returned.                               [default: 1]
  --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.