:py:mod:`biotaphy.tools.phylo_beta_diversity`
=============================================

.. py:module:: biotaphy.tools.phylo_beta_diversity

.. autoapi-nested-parse::

   Tool for computing beta diversity and phylo beta diversity.

   Args:
   1) file location of the PAM (presence absence matrix)
   2) file location of the tree associsated with PAM
   3) phylo beta diversity family to use
   4) file location to write output
   5) (optional) the number of permuatations to perform
   6) (optional) alpha value to determine significance (defaul = 0.05)

   .. todo::

      * Constants.
      * Clean up help.



Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   biotaphy.tools.phylo_beta_diversity.cli



Attributes
~~~~~~~~~~

.. autoapisummary::

   biotaphy.tools.phylo_beta_diversity.DESCRIPTION


.. py:data:: DESCRIPTION
   :annotation: = Multiline-String

    .. raw:: html

        <details><summary>Show Value</summary>

    .. code-block:: text
        :linenos:

        
        Computes phylogenetic & ecological beta diversity components for Sorensen and
        Jaccard Indices.

    .. raw:: html

        </details>

   

.. py:function:: cli()

   Command line interface for the tool.

   :raises ValueError: Raised for unknown format or missing family.