Who is Who in Phylogenetic Networks

Publication no #596   Type :   Html | Bib | Both

Created: 2007-12-28 14:36:46     Modified: 2008-04-03 01:17:34

596 Patricia Buendia and Giri Narasimhan. Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach. In BIO, Vol. 23(22):2993-3000, 2007. Keywords: from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software. Note: http://dx.doi.org/10.1093/bioinformatics/btm413.         Toggle abstract "Motivation: Traditional phylogenetic methods assume tree-like evolutionary models and are likely to perform poorly when provided with sequence data from fast-evolving, recombining viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data. A more general approach is proposed here, referred to as the Sliding MinPD method, that reconstructs evolutionary networks for serially-sampled sequences in the presence of recombination. Results: Sliding MinPD combines distance-based phylogenetic methods with automated recombination detection based on the best-known sliding window approaches to reconstruct serial evolutionary networks. Its performance was evaluated through comprehensive simulation studies and was also applied to a set of serially-sampled HIV sequences from a single patient. The resulting network organizations reveal unique patterns of viral evolution and may help explain the emergence of disease-associated mutants and drug-resistant strains with implications for patient prognosis and treatment strategies. © The Author 2007. Published by Oxford University Press. All rights reserved." @Article{BuendiaNarasimhan2007b,       AUTHOR = {Buendia, Patricia and Narasimhan, Giri},       TITLE = {Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach},       YEAR = {2007},       JOURNAL = {BIO},       VOLUME = {23},       NUMBER = {22},       PAGES = {2993-3000},       URL = {http://dx.doi.org/10.1093/bioinformatics/btm413},       NOTE = {http://dx.doi.org/10.1093/bioinformatics/btm413},       ANNOTE = {BIBUPDATE : 20071228},       KEYWORDS = {from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software} }