The PHYLIPNEW versions of these programs all have the prefix "f" to distinguish them from the original programs.
| Program name | Description | 
|---|---|
| fclique | Largest clique program | 
| fconsense | Majority-rule and strict consensus tree | 
| fcontml | Gene frequency and continuous character maximum likelihood | 
| fcontrast | Continuous character contrasts | 
| fdiscboot | Bootstrapped discrete sites algorithm | 
| fdnacomp | DNA compatibility algorithm | 
| fdnadist | Nucleic acid sequence distance matrix program | 
| fdnainvar | Nucleic acid sequence invariants method | 
| fdnaml | Estimate 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 | 
| fdollop | Dollo and polymorphism parsimony algorithm | 
| fdolmove | Interactive Dollo or polymorphism parsimony | 
| fdolpenny | Penny algorithm Dollo or polymorphism | 
| fdrawgram | Plots a cladogram- or phenogram-like rooted tree diagram | 
| fdrawtree | Plots an unrooted tree diagram | 
| ffactor | Multistate to binary recoding program | 
| ffitch | Fitch-Margoliash and least-squares distance methods | 
| ffreqboot | Bootstrapped genetic frequencies algorithm | 
| fgendist | Compute genetic distances from gene frequencies | 
| fkitsch | Fitch-Margoliash method with contemporary tips | 
| fmix | Mixed parsimony algorithm | 
| fmove | Interactive mixed method parsimony | 
| fneighbor | Phylogenies from distance matrix by N-J or UPGMA method | 
| fpars | Discrete character parsimony | 
| fpenny | Penny algorithm, branch-and-bound | 
| 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 | Calculate distance matrix from restriction sites or fragments | 
| frestml | Restriction site maximum likelihood method | 
| fretree | Interactive tree rearrangement | 
| fseqboot | Bootstrapped sequences algorithm | 
| fseqbootall | Bootstrapped sequences algorithm | 
| ftreedist | Calculate distances between trees | 
| ftreedistpair | Calculate distance between two sets of trees |