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Syst Biol. 2013 Jan 1;62(1):110-20. doi: 10.1093/sysbio/sys076. Epub 2012 Sep 4.

TreeFix: statistically informed gene tree error correction using species trees.

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1
Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Abstract

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.

PMID:
22949484
PMCID:
PMC3526801
DOI:
10.1093/sysbio/sys076
[Indexed for MEDLINE]
Free PMC Article
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