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).
--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.
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.
