fasttree: Construct a phylogenetic tree with FastTree.¶

Docstring:

Usage: qiime phylogeny fasttree [OPTIONS]

  Construct a phylogenetic tree with FastTree.

Inputs:
  --i-alignment ARTIFACT FeatureData[AlignedSequence]
                          Aligned sequences to be used for phylogenetic
                          reconstruction.                           [required]
Parameters:
  --p-n-threads NTHREADS  The number of threads. Using more than one thread
                          runs the non-deterministic variant of `FastTree`
                          (`FastTreeMP`), and may result in a different tree
                          than single-threading. See
                          http://www.microbesonline.org/fasttree/#OpenMP for
                          details. (Use `auto` to automatically use all
                          available cores)                        [default: 1]
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.