Dear all, Thanks a lot for your answers ! Here are the main references I obtained from you on choice for phylogeny methods / models : At first, some books : 1) Barry Hall. Phylogenetic Trees Made Easy: A How-To Manual Bellingham Research Institute ; Third Edition (Bayesian methods should be integrated in this version ; recommended twice) : http://www.sinauer.com/hall/3e/ 2) Page & Holmes. Molecular Evolution. A Phylogenetic Approach (recommended twice) http://www.amazon.com/Molecular-Evolution-Roderick-D-M-Page/dp/0865428891/ref=sr_1_5?ie=UTF8&qid=1326723824&sr=8-5 3) Hillis, Moritz, Mable. Molecular Systematics (recommended twice) "If you read through these three in order (or at least 1+2), you should get a solid foundation of understanding different methods and models and how to choose among them. I believe #1 has been updated to include Bayesian methods, but I'm not sure about #2+3." [ Jaret Bilewitch ] - The Phylogenetic Handbook A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, by P. Lemey, M. Salemi, A.M. Vandamme (recommended twice) http://www.amazon.com/Phylogenetic-Handbook-Practical-Approach-Hypothesis/dp/0521730716/ref=pd_sim_b_1 - Phylogenetics The theory and practice of phylogenetic systematics, by E.O. Wiley, - Inferring Phylogenies, Joseph Felsenstein : http://www.sinauer.com/detail.php?id=1775 - (in french :) Concepts et méthodes en phylogénie moléculaire Collection: Collection IRIS Perrière, Guy, Brochier-Armanet, Céline 1st Edition., 2010, XII, 250 p. http://www.springer.com/life+sciences/systems+biology+and+bioinformatics/book/978-2-287-99047-2 Then, some articles too : - Kelchner SA, Thomas MA. 2007. Model use in phylogenetics: nine key questions. Trends Ecol Evol. 22:87–94. - Papers written by Nei and Saitou explaining advantages and disadvantages of each type of method : Saitou N, Imanishi T (1989) Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol. 6(5):514-525. Takahashi K, Nei M (2000) Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol. Biol. Evol. 17(8): 1251-1258. Tateno Y, Takezaki N, Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11(2):261-277. - And for bayesian inference (BI) : Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJP (2003) Comparison of bayesian and maximum likelihood bootstrap measures of phylogenetic reliability Mol Biol Evol 20(2):248-254 Alfaro ME, Zoller S, Lutzoni F (2003) Bayes or bootstrap? A simulation study comparing the performance of bayesian Markov chain Monte Carlo sampling and bootstrappingin assessing phylogenetic confidence. Mol. Biol. Evol. 20(2): 255-266. Miscellaneous : - Workshops on phylogeny (recommended twice) : http://www.molecularevolution.org/ - In the documentation of the web server Phylemon2, the authors explain a roadmap that is normally used for phylogenetic studies and seems very interesting as a "lab protocol": http://docs.bioinfo.cipf.es/phylemonwiki/doku.php?id=phylemon:roadmap - Two programs on model choice within algorithm : . for models of maximum likelihood (ML) or BI, there is a program called jModelTest (http://darwin.uvigo.es/software/jmodeltest.html) that lets you choose the best model that fits your data when performing the phylogenetic tree in ML or BI. . to select between alternative substitution models, there is modelgenerator, available here (The paper is also listed there and they discuss in the paper the whole idea of comparing models) : http://bioinf.nuim.ie/modelgenerator/ Other advices : - "Talks with people, since a practical experience is sometimes needed in order to take a good decision. A secure approach remains a test of different methods, to see their impact on obtained results" [Céline Brochier ] - " You will find , as I found myself when I was in your position regarding phylogenetics methods, that no method or model it's bulletproof, and the selection or the point of view that most of the authors use to select the method are based on mere "personal philosophies" or trends. If you read a paper of P. Goloboff by example, it will talk wonders about Maximum Parsimony, but nowadays everybody want to include Bayesian method, or if they don’t understand quite the basics of the Bayesian theorem or application of the MCMC algorithm, they will use Maximum Likelihood. My recommendation is that if you are not quite sure of all the assumptions on EVERY method or model, use the one that you understand the most, or if you don't want to take that choice, analyze your sequences, if they have a lot of Parsimonious sites it will be advantageous to use Maximum Parsimony, or if you have a sequence very long (and don’t have a lot of sequence aligned) you can use maximum likelihood. Personally I don’t recommend using Bayesian method if you are just starting in the application of Phylogenetics. " [ Gabriel Golczer ] Hope it helps ! (and it does, undoubtedly) Thanks again to all of you (lot has not been cited here !) All the best, Gwennaël -------- Message original -------- Dear all, I am quite new in phylogeny and I know the very bases. I know some books about phylogeny, but they all seem to present phylogeny methods and distance matrices models without explaining how to make a good choice between those methods and models (though it is interesting to compare the results from different methods). My question is thus: do you know some interesting references (in English or in French) explaining practically how to select among phylogeny methods and models depending on your data ? Thank you very much in advance. Regards, Gwennaël -- Gwennaël BATAILLE, PhD student - Teaching assistant Earth and Life Institute Université Catholique de Louvain SST/ELI/ELIB Bâtiment Carnoy Croix du sud 4-5, bte L7.07.04 1348 Louvain-la-Neuve BELGIUM gwennael.bataille@uclouvain.be