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

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.