New EisenLab paper: PhyloSift: phylogenetic analysis of genomes and metagenomes [PeerJ]

New paper from people in the Eisen lab (and some others): PhyloSift: phylogenetic analysis of genomes and metagenomes [PeerJ].  This project was coordinated by Aaron Darling, who was a Project Scientist in my lab and is now a Professor at the University of Technology Sydney.  Also involved were Holly Bik (post doc in the lab), Guillaume Jospin (Bioinformatics Engineer in the lab), Eric Lowe (was a UC Davis undergrad working in the lab) and Erick Matsen (from the FHCRC).  This work was supported by a grant from the Department of Homeland Security.


Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection.

In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata.

These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).

For more about Phylosift see

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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