relatedness.py – Calculate NRI (net relatedness index) and NTI (nearest taxon index) using the formulas from Phylocom 4.2/3.41 and Webb 2002.

Description:

This script calculates NRI and NTI from a path to a Newick formatted tree and a path to a comma separated list of ids in that tree that form the group whose NRI/NTI you want to test. The tree is not required to have distances. If none are found script will use the number of nodes (self inclusive) as their distance from one another. NRI and NTI are calculated as described in the Phylocom manual (which is a slightly modified version of that found in Webb 2002, and Webb 2000). The Phylocom manual is freely available on the web and Webb 2002 can be found in the Annual Review of Ecology and Systematics: Phylogenies and Community Ecology Webb 2002.

Usage: relatedness.py [options]

Input Arguments:

Note

[REQUIRED]

-t, --tree_fp

The tree filepath

-g, --taxa_fp

Taxa list filepath

[OPTIONAL]

-i, --iters

Number of iterations to use for sampling tips without replacement (null model 2 community sampling, see see http://bodegaphylo.wikispot.org/Community_Phylogenetics). [default: 1000]

-m, --methods

Comma-separated list of metrics to calculate. [default: nri,nti]

-o, --output_fp

Path where output will be written [default: print to screen]

Output:

Outputs a value for specified tests

Calculate both NRI and NTI from the given tree and group of taxa:

relatedness.py -t reference.tre -g group1_otus.txt -m nri,nti

Calculate only NRI:

relatedness.py -t reference.tre -g group1_otus.txt -m nri

Calculate only NTI using a different number of iterations:

relatedness.py -t reference.tre -g group1_otus.txt -m nti -i 100

Calculate only NTI using a different number of iterations and save the results into a file called output.txt:

relatedness.py -t reference.tre -g group1_otus.txt -m nti -i 100 -o output.txt