| Program name | Description |
| distmat |
Create a distance matrix from a multiple sequence alignment
|
| 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
|