贝叶斯法

贝叶氏谱系分析
分类	演化生物学
子分类	分子系统发生学
最佳搜索条件	贝叶斯推断
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贝叶氏谱系分析（Bayesian inference of phylogeny）是根据已知的先验几率推导后验几率的似然函数，进而去预测最可能的系谱树。随着电脑计算速度的演进以及马尔科夫-蒙特卡洛法的演进，贝叶氏谱系分析越来越受重视和应用。贝叶斯推断时常应用于分子系统发生学以及系统分类学。

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分析软件列表

下表列出最常用的系谱分析软件，有些不只使用贝叶氏谱系分析。

更多信息 软件, 描述 ...

软件	描述	方法	作者	网址
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 ^[1]	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 ^[2]	http://www.bali-phy.org （页面存档备份，存于互联网档案馆）
BATWING	Bayesian Analysis of Trees With Internal Node Generation	Bayesian inference, demographic history, population splits	I. J. Wilson, D. Weale, D.Balding ^[3]	http://www.maths.abdn.ac.uk/˜ijw^{[永久失效链接]}
Bayes Phylogenies	Bayesian inference of trees using Markov Chain Monte Carlo methods	Bayesian inference, multiple models, mixture model (auto-partitioning)	M. Pagel, A. Meade ^[4]	http://www.evolution.rdg.ac.uk/BayesPhy.html （页面存档备份，存于互联网档案馆）
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 ^[5]	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 ^[6]	http://beast.bio.ed.ac.uk （页面存档备份，存于互联网档案馆）
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 ^[7]	http://www.stat.wisc.edu/~ane/bucky/ （页面存档备份，存于互联网档案馆）
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 （页面存档备份，存于互联网档案馆）
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.^[8]	http://www.topali.org （页面存档备份，存于互联网档案馆）

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应用

贝叶氏谱系分析在分子系统发生学上具有相当广泛的应用，包含：

系统发生学预测^[9]^[10]
预测及评估未明祖源^[11]
祖征演化^[12]^[13]
祖源地域推论^[14]
分子测年分析^[15]^[16]
物种多样化和灭绝的动力学模型^[17]
传染病扩散模型^[18]

参考文献

[1]
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
[2]
Suchard, M.A. and Redelings, B.D. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics. 22:2047-2048
[3]
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
[4]
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
[5]
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
[6]
Drummond, A.J., Rambaut, A. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214
[7]
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
[8]
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
[9]
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
[10]
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
[11]
de Villemereuil, P.,Wells, J.A., Edwards, R.D. and Blomberg, S.P. 2012. Bayesian Phylogeography Finds Its Roots BMC Evolutionary Biology 12:102
[12]
Ronquist, F. 2004. Bayesian inference of character Evolution. Trends in Ecology and Evolution 19 No.9: 475-481
[13]
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
[14]
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
[15]
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
[16]
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
[17]
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
[18]
Lemey, P., Rambaut, A., Drummond, A.J., Suchard, M.A. 2009. Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol 5(9): e1000520

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外部链接

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:贝叶氏导出式分析相关应用（英语：Category:Applications of Bayesian inference）

[1] [1]
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

[2] [2]
Suchard, M.A. and Redelings, B.D. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics. 22:2047-2048

[3] [3]
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

[4] [4]
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

[5] [5]
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

[6] [6]
Drummond, A.J., Rambaut, A. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214

[7] [7]
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

[8] [8]
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

[9] [9]
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

[10] [10]
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

[11] [11]
de Villemereuil, P.,Wells, J.A., Edwards, R.D. and Blomberg, S.P. 2012. Bayesian Phylogeography Finds Its Roots BMC Evolutionary Biology 12:102

[12] [12]
Ronquist, F. 2004. Bayesian inference of character Evolution. Trends in Ecology and Evolution 19 No.9: 475-481

[13] [13]
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

[14] [14]
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

[15] [15]
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

[16] [16]
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

[17] [17]
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

[18] [18]
Lemey, P., Rambaut, A., Drummond, A.J., Suchard, M.A. 2009. Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol 5(9): e1000520

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