The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring species trees from gene duplication episodes
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
A linear time algorithm for error-corrected reconciliation of unrooted gene trees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Algorithms for rapid error correction for the gene duplication problem
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Algorithms for knowledge-enhanced supertrees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Unrooted Tree Reconciliation: A Unified Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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