期刊
SYSTEMATIC BIOLOGY
卷 62, 期 1, 页码 110-120出版社
OXFORD UNIV PRESS
DOI: 10.1093/sysbio/sys076
关键词
Gene tree error correction; phylogenetics; reconciliation
资金
- Kambourides Fellowship
- National Science Foundation CAREER award [0644282]
- Direct For Biological Sciences [0644282] Funding Source: National Science Foundation
Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many important applications. However, sequence data alone often lack enough information to confidently support one gene tree topology over many competing alternatives. Here, we present a novel framework for combining sequence data and species tree information, and we describe an implementation of this framework in TreeFix, a new phylogenetic program for improving gene tree reconstructions. Given a gene tree (preferably computed using a maximum-likelihood phylogenetic program), TreeFix finds a statistically equivalent gene tree that minimizes a species tree-based cost function. We have applied TreeFix to 2 clades of 12 Drosophila and 16 fungal genomes, as well as to simulated phylogenies and show that it dramatically improves reconstructions compared with current state-of-the-art programs. Given its accuracy, speed, and simplicity, TreeFix should be applicable to a wide range of analyses and have many important implications for future investigations of gene evolution. The source code and a sample data set are available at http://compbio.mit.edu/treefix.
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