BEAST: Bayesian evolutionary analysis by sampling trees. Export

@article{citeulike:1888819, abstract = {BACKGROUND: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. RESULTS: BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. CONCLUSION: BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.}, author = {Drummond, Alexei J. and Rambaut, Andrew}, citeulike-article-id = {1888819}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2148-7-214}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17996036}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17996036}, doi = {10.1186/1471-2148-7-214}, issn = {1471-2148}, journal = {BMC evolutionary biology}, keywords = {algorithms, bayesian, markov-chains, methods, phylogeny, phyloinformatics, software, xml}, month = {November}, number = {1}, pages = {214+}, posted-at = {2009-05-22 07:02:11}, priority = {2}, title = {BEAST: Bayesian evolutionary analysis by sampling trees.}, url = {http://dx.doi.org/10.1186/1471-2148-7-214}, volume = {7}, year = {2007} }

TY - JOUR ID - citeulike:1888819 L3 - citeulike-article-id:1888819 N2 - BACKGROUND: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. RESULTS: BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. CONCLUSION: BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis. IS - 1 JF - BMC evolutionary biology SN - 1471-2148 TI - BEAST: Bayesian evolutionary analysis by sampling trees. VL - 7 SP - 214 KW - algorithms KW - bayesian KW - markov-chains KW - methods KW - phylogeny KW - phyloinformatics KW - software KW - xml AU - Drummond, Alexei AU - Rambaut, Andrew PY - 2007/11/08/ UR - http://dx.doi.org/10.1186/1471-2148-7-214 ER -