Bioinformatics · 2008 · 156 citations · 11 references
Life SciencesBioinformaticsEvolutionary BiologyGenomic Data AnalysisGenomicsPhylogeneticsGene Tree InferencePhylogenetic AnalysisPhylogenetic InferencePhylogenetic Tree ReconstructionSpecies Tree InferenceTree ReconciliationGene Tree ReconciliationGene Tree Species Tree ReconciliationGenome Scale PhylogeneticsGenome-wide Phylogenetic AnalysisHeuristicsParsimony-based Gene Tree InferenceSearch HeuristicsTree Searching Algorithms
UNLABELLED: 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
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Wayne P. Maddison · Systematic Biology · 1997 · 3K citations
GeneTree: comparing gene and species phylogenies using reconciled trees.
Roderic Page · Bioinformatics · 1998 · 244 citations · Full text