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robinson-foulds: Calculate Robinson-Foulds distance between phylogenetic trees.

Citations
  • David F Robinson and Leslie R Foulds. Comparison of phylogenetic trees. Mathematical biosciences, 53(1-2):131–147, 1981.

Docstring:

Usage: qiime phylogeny robinson-foulds [OPTIONS]

  Calculate the Robinson-Foulds symmetric difference metric between two or
  more phylogenetic trees.

Inputs:
  --i-trees ARTIFACTS... List[Phylogeny[Rooted | Unrooted]]
                          Phylogenetic trees to compare with Robinson-Foulds.
                          Rooting information and branch lengths are ignored
                          by this metric.                           [required]
Parameters:
  --p-labels TEXT...      Labels to use for the tree names in the distance
    List[Str]             matrix. If ommited, labels will be "tree_n" where
                          "n" ranges from 1..N. The number of labels must
                          match the number of trees.                [optional]
  --p-missing-tips TEXT Choices('error', 'intersect-all')
                          How to handle tips that are not shared between
                          trees. "error" will raise an error if the set of
                          tips is not identical between all input trees.
                          "intersect-all" will remove tips that are not shared
                          between all trees before computing distances beteen
                          trees.                            [default: 'error']
Outputs:
  --o-distance-matrix ARTIFACT
    DistanceMatrix        The distances between trees as a symmetric matrix.
                                                                    [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).
  --examples              Show usage examples and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.phylogeny.methods import robinson_foulds

Docstring:

Calculate Robinson-Foulds distance between phylogenetic trees.

Calculate the Robinson-Foulds symmetric difference metric between two or
more phylogenetic trees.

Parameters
----------
trees : List[Phylogeny[Rooted | Unrooted]]
    Phylogenetic trees to compare with Robinson-Foulds. Rooting information
    and branch lengths are ignored by this metric.
labels : List[Str], optional
    Labels to use for the tree names in the distance matrix. If ommited,
    labels will be "tree_n" where "n" ranges from 1..N. The number of
    labels must match the number of trees.
missing_tips : Str % Choices('error', 'intersect-all'), optional
    How to handle tips that are not shared between trees. "error" will
    raise an error if the set of tips is not identical between all input
    trees. "intersect-all" will remove tips that are not shared between all
    trees before computing distances beteen trees.

Returns
-------
distance_matrix : DistanceMatrix
    The distances between trees as a symmetric matrix.