DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

André Wehe; Mukul S Bansal; J Gordon Burleigh; Oliver Eulenstein

doi:10.1093/bioinformatics/btn230

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

Bioinformatics. 2008 Jul 1;24(13):1540-1. doi: 10.1093/bioinformatics/btn230. Epub 2008 May 12.

Authors

André Wehe¹, Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein

Affiliation

¹ Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

PMID: 18474508
DOI: 10.1093/bioinformatics/btn230

Abstract

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++.

Availability: DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms*
Base Sequence
Chromosome Mapping / methods*
Computer Simulation
DNA Mutational Analysis / methods*
Evolution, Molecular*
Models, Genetic*
Molecular Sequence Data
Phylogeny
Sequence Analysis, DNA / methods*
Software*