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unweighted-unifrac: Unweighted Unifrac

Citations

Docstring:

Usage: qiime diversity-lib unweighted-unifrac [OPTIONS]

  Compute Unweighted Unifrac for each sample in a feature table

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]      The feature table containing the samples for which
                          Unweighted Unifrac should be computed.    [required]
  --i-phylogeny ARTIFACT  Phylogenetic tree containing tip identifiers that
    Phylogeny[Rooted]     correspond to the feature identifiers in the table.
                          This tree can contain tip ids that are not present
                          in the table, but all feature ids in the table must
                          be present in this tree.                  [required]
Parameters:
  --p-threads VALUE Int % Range(1, None) | Str % Choices('auto')
                          The number of CPU threads to use in performing this
                          calculation. May not exceed the number of available
                          physical cores. If threads = 'auto', one thread will
                          be created for each identified CPU core on the host.
                                                                  [default: 1]
  --p-bypass-tips / --p-no-bypass-tips
                          In a bifurcating tree, the tips make up about 50%
                          of the nodes in a tree. By ignoring them,
                          specificity can be traded for reduced compute time.
                          This has the effect of collapsing the phylogeny, and
                          is analogous (in concept) to moving from 99% to 97%
                          OTUs                                [default: False]
Outputs:
  --o-distance-matrix ARTIFACT
    DistanceMatrix        Distance matrix for Unweighted Unifrac.   [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.diversity_lib.methods import unweighted_unifrac

Docstring:

Unweighted Unifrac

Compute Unweighted Unifrac for each sample in a feature table

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples for which Unweighted Unifrac
    should be computed.
phylogeny : Phylogeny[Rooted]
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
threads : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of CPU threads to use in performing this calculation. May
    not exceed the number of available physical cores. If threads = 'auto',
    one thread will be created for each identified CPU core on the host.
bypass_tips : Bool, optional
    In a bifurcating tree, the tips make up about 50% of the nodes in a
    tree. By ignoring them, specificity can be traded for reduced compute
    time. This has the effect of collapsing the phylogeny, and is analogous
    (in concept) to moving from 99% to 97% OTUs

Returns
-------
distance_matrix : DistanceMatrix
    Distance matrix for Unweighted Unifrac.