Who is Who in Phylogenetic Networks

Publication no #2010   Type :   Html | Bib | Both

Created: 2010-05-11 10:28:35     Modified: 2016-04-22 17:04:55

2010 Jean-Philippe Doyon, Celine Scornavacca, Konstantin Yu Gorbunov, Gergely J. Szöllösi, Vincent Ranwez and Vincent Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10), Vol. 6398:93-108 of LNCS, springer, 2011. Keywords: branch length, duplication, dynamic programming, explicit network, from multilabeled tree, from species tree, from unrooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Mowgli, reconstruction. Note: http://www.lirmm.fr/~vberry/Publis/MPR-DoyonEtAl.pdf, software available at http://www.atgc-montpellier.fr/MPR/.         Toggle abstract "Tree reconciliation methods aim at estimating the evolutionary events that cause discrepancy between gene trees and species trees. We provide a discrete computational model that considers duplications, transfers and losses of genes. The model yields a fast and exact algorithm to infer time consistent and most parsimonious reconciliations. Then we study the conditions under which parsimony is able to accurately infer such events. Overall, it performs well even under realistic rates, transfers being in general less accurately recovered than duplications. An implementation is freely available at http://www.atgc- montpellier.fr/MPR. © 2010 Springer-Verlag." @InProceedings{DSGSRB2010,       AUTHOR = {Doyon, Jean-Philippe and Scornavacca, Celine and Gorbunov, Konstantin Yu and Sz{\~A}�ll{\~A}�si, Gergely J. and Ranwez, Vincent and Berry, Vincent},       TITLE = {An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers},       YEAR = {2011},       BOOKTITLE = {Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10)},       VOLUME = {6398},       PAGES = {93-108},       SERIES = {LNCS},       PUBLISHER = {springer},       URL = {http://dx.doi.org/10.1007/978-3-642-16181-0_9},       NOTE = {http://www.lirmm.fr/~vberry/Publis/MPR-DoyonEtAl.pdf, software available at http://www.atgc-montpellier.fr/MPR/},       KEYWORDS = {branch length, duplication, dynamic programming, explicit network, from multilabeled tree, from species tree, from unrooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Mowgli, reconstruction} }