Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Minireview cung cấp cho các bạn kiến thức về ngành y đề tài: IA simple, fast, and accurate method of phylogenomic inference. | Open Access Mpthbd A simple fast and accurate method of phylogenomic inference Martin Wu and Jonathan A Eisen n Addresses Genome Center University of California One Shields Avenue Davis CA 95616 USA. Section of Evolution and Ecology College of Biological Sciences University of California One Shields Avenue Davis CA 95616 USA. Department of Medical Microbiology and Immunology School of Medicine University of California One Shields Avenue Davis CA 95616 USA. Correspondence Martin Wu. Email mwu2000@ Published 13 October 2008 Genome Biology 2008 9 R151 doi gb-2008-9- l0-rl5l The electronic version of this article is the complete one and can be found online at http 2008 9 l0 Rl5l Received 12 August 2008 Revised 26 September 2008 Accepted l3 October 2008 2008 Wu and Eisen licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. 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. Background Since the 1970s the use of small subunit SSU rRNA SSU rRNA sequences has revolutionized microbial classification systematics and ecology. The SSU rRNA gene has become the most sequenced gene with hundreds of thousands of its sequences now deposited in public databases. It has become the current gold standard in microbial .
