| Program name | Description | 
|---|
| distmat | Creates a distance matrix from multiple alignments | 
| ednacomp | DNA compatibility algorithm | 
| ednadist | Nucleic acid sequence Distance Matrix program | 
| ednainvar | Nucleic acid sequence Invariants method | 
| ednaml | Phylogenies from nucleic acid Maximum Likelihood | 
| ednamlk | Phylogenies from nucleic acid Maximum Likelihood with clock | 
| ednapars | DNA parsimony algorithm | 
| ednapenny | Penny algorithm for DNA | 
| eprotdist | Protein distance algorithm | 
| eprotpars | Protein parsimony algorithm | 
| erestml | Restriction site Maximum Likelihood method | 
| eseqboot | Bootstrapped sequences algorithm | 
| fdiscboot | Bootstrapped discrete sites algorithm | 
| fdnacomp | DNA compatibility algorithm | 
| fdnadist | Nucleic acid sequence Distance Matrix program | 
| fdnainvar | Nucleic acid sequence Invariants method | 
| fdnaml | Estimates nucleotide phylogeny by maximum likelihood | 
| fdnamlk | Estimates nucleotide phylogeny by maximum likelihood | 
| fdnamove | Interactive DNA parsimony | 
| fdnapars | DNA parsimony algorithm | 
| fdnapenny | Penny algorithm for DNA | 
| fdolmove | Interactive Dollo or Polymorphism Parsimony | 
| ffreqboot | Bootstrapped genetic frequencies algorithm | 
| fproml | Protein phylogeny by maximum likelihood | 
| fpromlk | Protein phylogeny by maximum likelihood | 
| fprotdist | Protein distance algorithm | 
| fprotpars | Protein parsimony algorithm | 
| frestboot | Bootstrapped restriction sites algorithm | 
| frestdist | Distance matrix from restriction sites or fragments | 
| frestml | Restriction site maximum Likelihood method | 
| fseqboot | Bootstrapped sequences algorithm | 
| fseqbootall | Bootstrapped sequences algorithm |