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fasttree: Construct a phylogenetic tree with FastTree.

Citations

[phylogeny:fasttree:PDA10]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.

Options:
  --i-alignment ARTIFACT PATH FeatureData[AlignedSequence]
                                  Aligned sequences to be used for
                                  phylogenetic reconstruction.  [required]
  --p-n-threads INTEGER RANGE     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 h
                                  ttp://www.microbesonline.org/fasttree/#OpenM
                                  P for details. (Use 0 to automatically use
                                  all available cores)  [default: 1]
  --o-tree ARTIFACT PATH Phylogeny[Unrooted]
                                  The resulting phylogenetic tree.  [required
                                  if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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.