Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm Export

@article{citeulike:875116, abstract = {The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative recombination events. The software implementation can be run quickly and efficiently in a distributed computing environment, and various components of the methods can be chosen for computational expediency or statistical rigor. We evaluate the performance of the new method on simulated alignments and on an array of published benchmark data sets. Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection. 10.1093/molbev/msl051}, author = {Kosakovsky Pond, Sergei L. and Posada, David and Gravenor, Michael B. and Woelk, Christopher H. and Frost, Simon D. W.}, citeulike-article-id = {875116}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/molbev/msl051}, citeulike-linkout-1 = {http://mbe.oxfordjournals.org/content/23/10/1891.abstract}, citeulike-linkout-2 = {http://mbe.oxfordjournals.org/content/23/10/1891.full.pdf}, citeulike-linkout-3 = {http://mbe.oxfordjournals.org/cgi/content/abstract/23/10/1891}, citeulike-linkout-4 = {http://www.ingentaconnect.com/content/oup/molbev/2006/00000023/00000010/art01891}, citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/16818476}, citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=16818476}, day = {1}, doi = {10.1093/molbev/msl051}, issn = {0737-4038}, journal = {Mol Biol Evol}, keywords = {phylogenetic, recombination, these, tree}, month = {October}, number = {10}, pages = {1891--1901}, posted-at = {2009-11-05 15:54:47}, priority = {2}, publisher = {Oxford University Press}, title = {Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm}, url = {http://dx.doi.org/10.1093/molbev/msl051}, volume = {23}, year = {2006} }

TY - JOUR ID - citeulike:875116 L3 - citeulike-article-id:875116 N2 - The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative recombination events. The software implementation can be run quickly and efficiently in a distributed computing environment, and various components of the methods can be chosen for computational expediency or statistical rigor. We evaluate the performance of the new method on simulated alignments and on an array of published benchmark data sets. Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection. 10.1093/molbev/msl051 IS - 10 JF - Mol Biol Evol SN - 0737-4038 EP - 1901 TI - Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm PB - Oxford University Press VL - 23 SP - 1891 KW - phylogenetic KW - recombination KW - these KW - tree AU - Kosakovsky Pond, Sergei AU - Posada, David AU - Gravenor, Michael AU - Woelk, Christopher AU - Frost, Simon PY - 2006/10/01/ UR - http://dx.doi.org/10.1093/molbev/msl051 ER -