| AAToInt | AA, DNA, RNA character set |
| GONNET | The GONNET AA matrix |
| optim.phylo.wls | Phylogeny inference using the weighted least squares method |
| PAMn | PAM and Dayhoff matrices calculation |
| TKF91 | Evolutionary distance estimation with TKF91 model |
| TKF92 | Evolutionary distance estimation with TKF92 model |
| TKF92HG | Evolutionary distance estimation with TKF92 model considering... |
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