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来自维基百科,自由的百科全书
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。
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) |
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:
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