Phylogenetic Organization of Metagenomic Signals

Code to identify functional enrichments across diverse taxa in phylogenetic tree, particularly where these taxa differ in abundance across samples in a non-random pattern. The motivation for this approach is to identify microbial functions encoded by diverse taxa that are at higher abundance in certain samples compared to others, which could indicate that such functions are broadly adaptive under certain conditions. See 'GitHub' repository for tutorial and examples: < https://github.com/gavinmdouglas/POMS/wiki>. Citation: Gavin M. Douglas, Molly G. Hayes, Morgan G. I. Langille, Elhanan Borenstein (2022) .

This repository corresponds to the joint taxa-function analysis tool Phylogenetic Organization of Metagenomic Signals (POMS), described in this paper:

Gavin M. Douglas, Molly G. Hayes, Morgan G. I. Langille, Elhanan Borenstein. 2022. Integrating phylogenetic and functional data in microbiome studies. Bioinformatics 38 (22):5055-5063.

This tool is for identifying functions (e.g., microbial gene families) that are encoded by disparate taxa that differ in abundance in the same sample direction. Such functions are referred to as consistently enriched functions, which could represent functions that are adaptive for many taxa in a given environment.

All feedback is appreciated! Please open an issue on this repository if you would like to ask a question or make a comment.

The POMS documentation is found on the wiki site.