A simple, fast, and accurate method of phylogenomic inference

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


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Databases, Genetic
  • Genome, Bacterial*
  • Genomics / methods*
  • Phylogeny*
  • Sequence Alignment