| 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 |
[45ā47] | 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] |
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