 The study presents an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis including Bayesian hypothesis tests for the presence of an organism in a sample, comparison of community structure across a collection of many samples, and association between the abundance of certain organisms and sample metadata. These analyses are implemented in an open-source software pipeline called Phylocift which incorporates several other programs to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms. This article was authored by Ernie Darling, Guillaume Jospin, Eric Lowe, and others.