Simultaneous statistical multiple alignment and phylogeny reconstruction. Export

@article{citeulike:735702, abstract = {Although the reconstruction of phylogenetic trees and the computation of multiple sequence alignments are highly interdependent, these two areas of research lead quite separate lives, the former often making use of stochastic modeling, whereas the latter normally does not. Despite the fact that reasonable insertion and deletion models for sequence pairs were already introduced more than 10 years ago, they have only recently been applied to multiple alignment and only in their simplest version. In this paper we present and discuss a strategy based on simulated annealing, which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences'indel history, i.e., their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree. Our method is also the first application of the TKF2 model in the context of multiple sequence alignment. We validate the method via simulations and illustrate it using a data set of primate mtDNA.}, address = {Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho Moscow, Idaho 83844-1103, USA. fleissne@uidaho.edu}, author = {Fleissner, R. and Metzler, D. and von Haeseler, A.}, citeulike-article-id = {735702}, citeulike-linkout-0 = {http://dx.doi.org/10.1080/10635150590950371}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16085574}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16085574}, doi = {10.1080/10635150590950371}, issn = {1063-5157}, journal = {Syst Biol}, keywords = {statisticalalignment}, month = {August}, number = {4}, pages = {548--561}, posted-at = {2006-07-04 01:26:01}, priority = {2}, title = {Simultaneous statistical multiple alignment and phylogeny reconstruction.}, url = {http://dx.doi.org/10.1080/10635150590950371}, volume = {54}, year = {2005} }

TY - JOUR ID - citeulike:735702 L3 - citeulike-article-id:735702 N2 - Although the reconstruction of phylogenetic trees and the computation of multiple sequence alignments are highly interdependent, these two areas of research lead quite separate lives, the former often making use of stochastic modeling, whereas the latter normally does not. Despite the fact that reasonable insertion and deletion models for sequence pairs were already introduced more than 10 years ago, they have only recently been applied to multiple alignment and only in their simplest version. In this paper we present and discuss a strategy based on simulated annealing, which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences'indel history, i.e., their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree. Our method is also the first application of the TKF2 model in the context of multiple sequence alignment. We validate the method via simulations and illustrate it using a data set of primate mtDNA. IS - 4 JF - Syst Biol SN - 1063-5157 AD - Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho Moscow, Idaho 83844-1103, USA. fleissne@uidaho.edu EP - 561 TI - Simultaneous statistical multiple alignment and phylogeny reconstruction. VL - 54 SP - 548 KW - statisticalalignment AU - Fleissner, R AU - Metzler, D AU - von Haeseler, A PY - 2005/08// UR - http://dx.doi.org/10.1080/10635150590950371 ER -