A simple, fast, and accurate method of phylogenomic inference

Martin Wu, Jonathan A Eisen

Research output: Contribution to journalArticlepeer-review

345 Scopus citations


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.

Original languageEnglish (US)
Article numberR151
JournalGenome Biology
Issue number10
StatePublished - Oct 13 2008

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics


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