贝叶斯法

贝叶氏谱系分析（Bayesian inference of phylogeny）是根据已知的先验机率推导后验机率的似然函数，进而去预测最可能的系谱树。随著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。

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
查 论 编

分析软体列表

下表列出最常用的系谱分析软体，有些不只使用贝叶氏谱系分析。

软体	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）

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：

BEAST以分子时钟分析法（molecular clock analysis）得出的系谱树。圆饼图表示的是利用贝叶氏二元MCMC分析（BBM）所推断的祖源。

• 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]