Journal
GENOME BIOLOGY
Volume 9, Issue 10, Pages -Publisher
BMC
DOI: 10.1186/gb-2008-9-10-r151
Keywords
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Funding
- NSF [DEB-0228651]
- Gordon and Betty Moore Foundation [1660]
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The explosive growth of genomic data provides an opportunity for increased usage of protein markers for phylogenetic inference. In response, 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.
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