TreeFix: statistically informed gene tree error correction using species trees.
TreeFix: statistically informed gene tree error correction using species trees.
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DOI：
10.1093/sysbio/sys076
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发表时间：
2013-01-01
影响因子：
6.5
通讯作者：
Kellis M
中科院分区：
文献类型：
--
作者：
Wu YC;Rasmussen MD;Bansal MS;Kellis M
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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影响因子：
4.5
作者：
Hahn MW;Han MV;Han SG
通讯作者：
Han SG
影响因子：
6.5
作者：
PAGE, RDM
通讯作者：
PAGE, RDM
影响因子：
12.3
作者：
Hahn, Matthew W.
通讯作者：
Hahn, Matthew W.
影响因子：
6.5
作者：
Maddison, WP
通讯作者：
Maddison, WP
影响因子：
10.7
作者：
Ness, Rob W.;Graham, Sean W.;Barrett, Spencer C. H.
通讯作者：
Barrett, Spencer C. H.