Branch-and-Bound Approach for Parsimonious Inference of a Species Tree from a Set of Gene Family Trees
We describe a Branch-and-Bound algorithm for computing a parsimonious species tree, given a set of gene family trees. Our algorithm can consider three cost measures: number of gene duplications, number of gene losses, and both combined. Moreover, to cope with intrinsic limitations of Branch-and-Bound algorithms for species trees inference regarding the number of taxa that can be considered, our algorithm can naturally take into account predefined relationships between sets of taxa. We test our algorithm on a dataset of eukaryotic gene families spanning 29 taxa.
KeywordsComparative genomics Evolution and phylogenetics
- 3.C. Chauve and N. El-Mabrouk. New perspectives on gene family evolution: Losses in reconciliation and a link with supertrees. In Research in Computational Molecular Biology, 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings, volume 5541 of Lecture Notes in Computer Science, pages 46–58. Springer, 2009.Google Scholar
- 4.J.P. Doyon and C. Chauve. Branch-and-bound approach for parsimonious inference of a species tree from a set of gene family trees. Technical report, LIRMM, 2010. URL http://hal-lirmm.ccsd.cnrs.fr/lirmm-00448481/fr/.
- 7.M.T. Hallett and J. Lagergren. New algorithms for the duplication-loss model. In Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, April 8-11, 2000, Tokyo, Japan, pages 138–146. ACM Press, 2000.Google Scholar
- 12.A. Wehe, M.S. Bansal, J.G Burleigh, and O. Eulenstein. DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics, 24(13):1540–1541, 2008.Google Scholar