Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

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]