Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees Export

@article{citeulike:4900854, abstract = {Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SATe (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies. 10.1126/science.1171243}, author = {Liu, Kevin and Raghavan, Sindhu and Nelesen, Serita and Linder, C. Randal and Warnow, Tandy}, citeulike-article-id = {4900854}, citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1171243}, citeulike-linkout-1 = {http://www.sciencemag.org/content/324/5934/1561.abstract}, citeulike-linkout-2 = {http://www.sciencemag.org/content/324/5934/1561.full.pdf}, citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/324/5934/1561}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19541996}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19541996}, doi = {10.1126/science.1171243}, journal = {Science}, keywords = {evolution, phylogenetics, tree}, month = {June}, number = {5934}, pages = {1561--1564}, posted-at = {2009-07-03 21:51:46}, priority = {2}, title = {Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees}, url = {http://dx.doi.org/10.1126/science.1171243}, volume = {324}, year = {2009} }

TY - JOUR ID - citeulike:4900854 L3 - citeulike-article-id:4900854 N2 - Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SATe (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies. 10.1126/science.1171243 IS - 5934 JF - Science EP - 1564 TI - Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees VL - 324 SP - 1561 KW - evolution KW - phylogenetics KW - tree AU - Liu, Kevin AU - Raghavan, Sindhu AU - Nelesen, Serita AU - Linder, Randal AU - Warnow, Tandy PY - 2009/06/19/ UR - http://dx.doi.org/10.1126/science.1171243 ER -