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

NameMethodPlatformGUIInferenceReference

BAMBEBayesDOS, MacOS, UnixNoTree [36]
BayesPhylogeniesBayesDOS, MacOS, UnixNoTree [37]
BAli-PhyBayesDOS, MacOS, UnixNoSimultaneous alignment and tree [38]
BEASTBayesWindows, MacOS, UnixYesTree, times [39]
CONSELMLDOS, MacOS, UnixNoTree comparison [40]
DAMBEDistances, parsimony, MLWindowsYesTree [29]
GARLIML (Genetic Algorithm)Windows, MacOS, UnixYesTree [41]
HyPhyMLWindows, MacOS, UnixYesTree, selection, recombination, tree comparison,[42]
MEGADistances, parsimonyWindowsYesTree, times [30, 31]
MrBayesBayesDOS, MacOS, UnixNoTree, selection [43, 44]
MultidivtimeBayesDOS, MacOS, UnixNoTimes [4547]
OmegaMapBayesDOS, MacOS, UnixNoSimultaneous selection and recombination[48]
PAMLMLDOS, MacOS, UnixNoTree, tree comparison, times, selection[49, 50]
PAUP*Distances, parsimony, MLDOS, MacOS, UnixNoTree [51]
PhyloBayesBayesDOS, MacOS, UnixNoTree, tree comparison [52]
PHYMLMLDOS, MacOS, UnixNoTree [53]
RAxMLMLDOS, MacOS, UnixNoTree [54]
r8sPLDOS, MacOS, UnixNoTimes [55]