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Genome Biol. 2008 Oct 13;9(10):R151. doi: 10.1186/gb-2008-9-10-r151.

A simple, fast, and accurate method of phylogenomic inference.

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1
Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA. mwu2000@gmail.com

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.

PMID:
18851752
PMCID:
PMC2760878
DOI:
10.1186/gb-2008-9-10-r151
[Indexed for MEDLINE]
Free PMC Article
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