利用mlbi法构建系统发育树.pdfVIP

利用ML、BI 法构建系统发育树 4.2 jModelTest jModelTest is a scientific application that can perform a selection of nucleotide substitutions, useful in DNA analysis, with support for large packets of data. 最新版本：2.1.7 （2015.12.18 ） 软件主页：/get/Science-CAD/jModelTest.shtml /p/jmodeltest2/ 讨论组：/group/jmodeltest TCS 的作者David Posada （西班牙Vigo 大学）开发的另一软件 Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772. Guindon S and Gascuel O (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52: 696-704. jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch lenght), heuristic filtering and automatic logging of user activity. （1）Introduction 对于ML、贝叶斯分析，需要选择合适的核苷酸替代模型，由于不同来源的基因片段具 有不同的生物学特性，所以不同片段的最适模型也不尽相同，对于联合片段其进化模型也需 要进行选择，并在联合分析时将得到的最优模型用于贝叶斯分析。一般对于单一片段可用 jModelTest 来算，而联合片段需要用PMT 软件来分段计算（见后）。 jModelTest 0.1.1 前身是ModelTest 3.7 ，用于为贝叶斯分析等选择最合适的核苷酸替换 模型。共有88 个模型（ModelTest 有64 个模型），可运行5 种模型选择策略（打分方法）： hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision