贝叶斯法

貝葉氏譜系分析（Bayesian inference of phylogeny）是根據已知的先驗機率推導後驗機率的似然函數，進而去預測最可能的系譜樹。隨著電腦計算速度的演進以及马尔科夫-蒙特卡洛法的演進，貝葉氏譜系分析越來越受重視和應用。贝叶斯推断時常應用於分子系統發生學以及系統分類學。 下表列出最常用的系譜分析軟體，有些不只使用貝葉氏譜系分析。 貝葉氏譜系分析在分子系統發生學上具有相當廣泛的應用，包含： 系統發生學預測 預測及評估未明祖源 祖徵演化 祖源地域推論 分子測年分析 物種多樣化和滅絕的動力學模型 傳染病擴散模型 Lord, E., Leclercq, M., Boc, A., Diallo, A.B., Makarenkov, V. 2012. Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations. PLoS ONE 7(1): e29903. doi:10.1371/journal.pone.0029903 Suchard, M.A. and Redelings, B.D. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics. 22:2047-2048 Wilson, I., Weale, D. and Balding, M. 2003. Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. Journal of the Royal Statistical Society: Series A (Statistics in Society), 166: 155-188 Pagel, M. and Meade, A. 2006. Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. American Naturalist, 167, 808-825 Lartillot N., Philippe H. 2004. A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process. Molecular Biology and Evolution 21(6):1095-1109 Drummond, A.J., Rambaut, A. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214 Ané, C., Larget, B., Baum, D.A.,Smith, S.D., Rokas, A. 2007. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24(2), 412-426 Milne, I., Lindner, D., Bayer, M., Husmeier, D., McGuire, G., Marshall, D.F. and Wright, F. 2008. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25 (1), 126-127 Alonso, R., Crawford, A.J. & Bermingham, E. 2011. Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes. Journal of Biogeography 39 (3): 434-451 Antonelli, A., Sanmart.n, I. 2011. Mass Extinction, Gradual Cooling, or Rapid Radiation? Reconstructing the Spatiotemporal Evolution of the Ancient Angiosperm Genus Hedyosmum (Chloranthaceae) Using Empirical and Simulated Approaches. Syst. Biol. 60(5):596–615 de Villemereuil, P.,Wells, J.A., Edwards, R.D. and Blomberg, S.P. 2012. Bayesian Phylogeography Finds Its Roots BMC Evolutionary Biology 12:102 Ronquist, F. 2004. Bayesian inference of character Evolution. Trends in Ecology and Evolution 19 No.9: 475-481 Schäffer , S., Koblmüller, S., Pfingstl, T., Sturmbauer, C., Krisper, G. 2010. Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the “Higher Oribatida” (Acari), conflicting with current classification schemes. BMC Evolutionary Biology 10:246 Filipowicz, N., Renner, S. 2012. Brunfelsia (Solanaceae): A genus evenly divided between South America and radiations on Cuba and other Antillean islands. Molecular Phylogenetics and Evolution 64: 1-11 Bacon, C.D., Baker, W.J., Simmons, M.P. 2012a. Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae). Systematic Biology 61: 426–442 Särkinen, T., Bohs, L., Olmstead,R.G. and Knapp, S. 2013. A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evolutionary Biology. 13:214 Silvestro, D., Schnitzler, J., Liow, L.H., Antonelli, A., Salamin, N. 2014. Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data. Syst. Biol. 63(3):349–367 Lemey, P., Rambaut, A., Drummond, A.J., Suchard, M.A. 2009. Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol 5(9): e1000520 MrBayes official website （页面存档备份，存于互联网档案馆） BEAST official website （页面存档备份，存于互联网档案馆） Template:Phylogenetics Category:貝葉氏導出式分析相關應用（英语：Category:Applications of Bayesian inference）