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fasttree: Construct a phylogenetic tree with FastTree.

Citations
  • Morgan N Price, Paramvir S Dehal, and Adam P Arkin. Fasttree 2–approximately maximum-likelihood trees for large alignments. PloS one, 5(3):e9490, 2010. doi:10.1371/journal.pone.0009490.

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 INTEGER   The number of threads. Using more than one thread
    Range(0, None)        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 0 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).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.phylogeny.methods import fasttree

Docstring:

Construct a phylogenetic tree with FastTree.

Construct a phylogenetic tree with FastTree.

Parameters
----------
alignment : FeatureData[AlignedSequence]
    Aligned sequences to be used for phylogenetic reconstruction.
n_threads : Int % Range(0, None), optional
    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 0 to
    automatically use all available cores)

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