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。

貝葉氏譜系分析

分類	演化生物学
子分類	分子系統發生學
最佳搜索條件	贝叶斯推断
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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 [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[永久失效連結]
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）

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：

BEAST以分子時鐘分析法（molecular clock analysis）得出的系譜樹。圓餅圖表示的是利用貝葉氏二元MCMC分析（BBM）所推斷的祖源。

• 系統發生學預測^[9][10]
• 預測及評估未明祖源^[11]
• 祖徵演化^[12][13]
• 祖源地域推論^[14]
• 分子測年分析^[15][16]
• 物種多樣化和滅絕的動力學模型^[17]
• 傳染病擴散模型^[18]