贝叶斯法
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 |
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 [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:
參考文獻
- ^ 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
- ^ Suchard, M.A. and Redelings, B.D. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics. 22:2047-2048
- ^ 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
- ^ 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
- ^ 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
- ^ Drummond, A.J., Rambaut, A. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214
- ^ 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
- ^ 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
- ^ 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
- ^ 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
- ^ de Villemereuil, P.,Wells, J.A., Edwards, R.D. and Blomberg, S.P. 2012. Bayesian Phylogeography Finds Its Roots BMC Evolutionary Biology 12:102
- ^ Ronquist, F. 2004. Bayesian inference of character Evolution. Trends in Ecology and Evolution 19 No.9: 475-481
- ^ 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
- ^ 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
- ^ 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
- ^ 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
- ^ 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
- ^ Lemey, P., Rambaut, A., Drummond, A.J., Suchard, M.A. 2009. Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol 5(9): e1000520