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A simple, fast, and accurate method of phylogenomic inference

Martin Wu1* and Jonathan A Eisen123

Author Affiliations

1 Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA

2 Section of Evolution and Ecology, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA

3 Department of Medical Microbiology and Immunology, School of Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA

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Genome Biology 2008, 9:R151  doi:10.1186/gb-2008-9-10-r151

Published: 13 October 2008

Abstract

The explosive growth of genomic data provides an opportunity to make increased use of protein markers for phylogenetic inference. We have developed an automated pipeline for phylogenomic analysis (AMPHORA) that overcomes the existing bottlenecks limiting large-scale protein phylogenetic inference. We demonstrated its high throughput capabilities and high quality results by constructing a genome tree of 578 bacterial species and by assigning phylotypes to 18,607 protein markers identified in metagenomic data collected from the Sargasso Sea.