title: TreeFix: statistically informed gene tree error correction using species trees.
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.
authors.affiliation: Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Yi-Chieh
authors.initials: YC
authors.lastname: Wu
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Rasmussen
authors.forename: Mukul S
authors.initials: MS
authors.lastname: Bansal
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
mesh_terms: D000818:Animals; D002965:Classification / Q000379:methods*; D004330:Drosophila / Q000145:classification / Q000235:genetics; D005658:Fungi / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D015203:Reproducibility of Results; D012984:Software