biotaphy.tools.phylo_beta_diversity

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)

Module Contents

Functions

cli()

Command line interface for the tool.

Attributes

DESCRIPTION

biotaphy.tools.phylo_beta_diversity.DESCRIPTION = Multiline-String[source]
Show Value
1 Computes phylogenetic & ecological beta diversity components for Sorensen and
2 Jaccard Indices.
biotaphy.tools.phylo_beta_diversity.cli()[source]

Command line interface for the tool.

Raises

ValueError – Raised for unknown format or missing family.