beta-phylogenetic: Beta diversity (phylogenetic)¶

Docstring:

Usage: qiime diversity beta-phylogenetic [OPTIONS]

  Computes a user-specified phylogenetic beta diversity metric for all pairs
  of samples in a feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]      The feature table containing the samples over which
                          beta diversity 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-metric TEXT Choices('generalized_unifrac', 'unweighted_unifrac',
    'weighted_normalized_unifrac', 'weighted_unifrac')
                          The beta diversity metric to be computed. [required]
  --p-threads NTHREADS    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-variance-adjusted / --p-no-variance-adjusted
                          Perform variance adjustment based on Chang et al.
                          BMC Bioinformatics 2011. Weights distances based on
                          the proportion of the relative abundance represented
                          between the samples at a given node under
                          evaluation.                         [default: False]
  --p-alpha PROPORTION Range(0, 1, inclusive_end=True)
                          This parameter is only used when the choice of
                          metric is generalized_unifrac. The value of alpha
                          controls importance of sample proportions. 1.0 is
                          weighted normalized UniFrac. 0.0 is close to
                          unweighted UniFrac, but only if the sample
                          proportions are dichotomized.             [optional]
  --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        The resulting distance 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).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --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.