title: DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
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++.
  
  
  BACKGROUND
  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
authors.affiliation: Department of Computer Science, Iowa State University, Ames, IA 50011, USA.
authors.forename: André
authors.initials: A
authors.lastname: Wehe
authors.forename: Mukul S
authors.initials: MS
authors.lastname: Bansal
authors.forename: J Gordon
authors.initials: JG
authors.lastname: Burleigh
authors.forename: Oliver
authors.initials: O
authors.lastname: Eulenstein
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004252:DNA Mutational Analysis / Q000379:methods*; D019143:Evolution, Molecular; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software