DupTree

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Summary: 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 .Contact: oeulenst@cs.iastate.edu


References in zbMATH (referenced in 4 articles )

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  1. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  2. Bayzid, Md. Shamsuzzoha; Warnow, Tandy: Gene tree parsimony for incomplete gene trees (2017)
  3. Ouangraoua, Aïda; Swenson, Krister M.; Chauve, Cedric: An approximation algorithm for computing a parsimonious first speciation in the gene duplication model (2010)
  4. Wehe, André; Bansal, Mukul S.; Burleigh, J. Gordon; Eulenstein, Oliver: Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. (2008) ioport