 PhiloSift is an open-source software pipeline designed to facilitate phylogenetic analysis of metagenomics data. It uses existing programs like LAST, HMR, and Placer to automate the process of analyzing protein coding and RNA sequences from metagenome datasets generated by modern sequencing platforms, Illumina, 454. The pipeline allows users to perform phylogenetic hypothesis testing, compare community structure across multiple samples, and identify associations between the abundances of certain organisms and sample metadata. This article was authored by Aaron E. Darling, Guillaume Jospin, Eric Lowe, and others.