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。
分析軟體列表
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。

軟體 描述  方法  作者  網址Armadillo Workflow Platform  Workflow platform dedicated to phylogenetic and general bioinformatic analysis  Inference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflows  E. Lord, M. Leclercq, A. Boc, A.B. Diallo and V. Makarenkov 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  https://web.archive.org/web/20161024081942/http://www.bioinfo.uqam.ca/armadillo/.Bali-Phy  Simultaneous Bayesian inference of alignment and phylogeny   Bayesian inference, alignment as well as tree search  M.A. Suchard, B. D. Redelings Suchard, M.A. and Redelings, B.D. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics. 22:2047-2048  http://www.bali-phy.org BATWING  Bayesian Analysis of Trees With Internal Node Generation  Bayesian inference, demographic history, population splits  I. J. Wilson, D. Weale, D.Balding 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  http://www.maths.abdn.ac.uk/˜ijw Bayes Phylogenies  Bayesian inference of trees using Markov Chain Monte Carlo methods  Bayesian inference, multiple models, mixture model (auto-partitioning)  M. Pagel, A. Meade  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  http://www.evolution.rdg.ac.uk/BayesPhy.html PhyloBayes / PhyloBayes MPI  Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction.  Non-parametric methods for modeling among-site variation in nucleotide or amino-acid propensities.  N. Lartillot, N. Rodrigue, D. Stubbs, J. Richer  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  https://web.archive.org/web/20181218053945/http://www.phylobayes.org/ BEAST  Bayesian Evolutionary Analysis Sampling Trees  Bayesian inference, relaxed molecular clock, demographic history  A. J. Drummond, A. Rambaut & M. A. Suchard Drummond, A.J., Rambaut, A. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214  http://beast.bio.ed.ac.uk  BUCKy  Bayesian concordance of gene trees  Bayesian concordance using modified greedy consensus of unrooted quartets  C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas and B. Larget, S.K. Kotha, C.N. Dewey, C. Ané 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  http://www.stat.wisc.edu/~ane/bucky/ Geneious (MrBayes plugin)  Geneious provides genome and proteome research tools  Neighbor-joining, UPGMA, MrBayes plugin, PHYML plugin, RAxML plugin, FastTree plugin, GARLi plugin, PAUP* Plugin  A. J. Drummond,M.Suchard,V.Lefort et al.  http://www.geneious.com  TOPALi  Phylogenetic inference  Phylogenetic model selection, Bayesian analysis and Maximum Likelihood phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis  I.Milne, D.Lindner, et al.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  http://www.topali.org 

 應用 
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): 434-451Antonelli, 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
 預測及評估未明祖源de Villemereuil, P.,Wells, J.A., Edwards, R.D. and Blomberg, S.P. 2012. Bayesian Phylogeography Finds Its Roots BMC Evolutionary Biology 12:102
祖徵演化Ronquist, F. 2004. Bayesian inference of character Evolution. Trends in Ecology and Evolution 19 No.9: 475-481Schäffer , 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
 祖源地域推論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
 分子測年分析Bacon, C.D., Baker, W.J., Simmons, M.P. 2012a. Miocene dispersal drives island radiations in the
palm tribe Trachycarpeae (Arecaceae). Systematic Biology 61: 426–442Särkinen, 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
 物種多樣化和滅絕的動力學模型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
 傳染病擴散模型Lemey, P., Rambaut, A., Drummond, A.J., Suchard, M.A. 2009. Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol 5(9): e1000520

 參考文獻 

 外部連結
 MrBayes official website 
 BEAST official website 

Category:貝氏推論
Category:生物信息學
Category:计算系统发生学