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Table 1: List of programs cited in this review. GUI: graphic user interface; ML: maximum likelihood; PL: penalized likelihood.

Name Method Platform GUI Inference Reference BAMBE Bayes DOS, MacOS, Unix No Tree [36] BayesPhylogenies Bayes DOS, MacOS, Unix No Tree [37] BAli-Phy Bayes DOS, MacOS, Unix No Simultaneous alignment and tree [38] BEAST Bayes Windows, MacOS, Unix Yes Tree, times [39] CONSEL ML DOS, MacOS, Unix No Tree comparison [40] DAMBE Distances, parsimony, ML Windows Yes Tree [29] GARLI ML (Genetic Algorithm) Windows, MacOS, Unix Yes Tree [41] HyPhy ML Windows, MacOS, Unix Yes Tree, selection, recombination, tree comparison, [42] MEGA Distances, parsimony Windows Yes Tree, times [30, 31] MrBayes Bayes DOS, MacOS, Unix No Tree, selection [43, 44] Multidivtime Bayes DOS, MacOS, Unix No Times [45–47] OmegaMap Bayes DOS, MacOS, Unix No Simultaneous selection and recombination [48] PAML ML DOS, MacOS, Unix No Tree, tree comparison, times, selection [49, 50] PAUP* Distances, parsimony, ML DOS, MacOS, Unix No Tree [51] PhyloBayes Bayes DOS, MacOS, Unix No Tree, tree comparison [52] PHYML ML DOS, MacOS, Unix No Tree [53] RAxML ML DOS, MacOS, Unix No Tree [54] r8s PL DOS, MacOS, Unix No Times [55]