| AAToInt | AA, DNA, RNA character set | 
| GONNET | The GONNET AA matrix | 
| optim.phylo.wls | Phylogeny inference using the weighted least squares distance... | 
| 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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