fdnadist         Nucleic acid sequence distance matrix program
fprotdist        Protein distance algorithm
fgendist         Compute genetic distances from gene frequencies
fclique          Largest clique program
fconsense        Majority-rule and strict consensus tree
fcontml          Gene frequency and continuous character Maximum Likelihood
fcontrast        Continuous character contrasts
fdnacomp         DNA compatibility algorithm
fdnainvar        Nucleic acid sequence invariants method
fdnaml           Estimates nucleotide phylogeny by maximum likelihood
fdnamlk          Estimates nucleotide phylogeny by maximum likelihood
fproml           Protein phylogeny by maximum likelihood
fpromlk          Protein phylogeny by maximum likelihood
frestml          Restriction site maximum Likelihood method
fdollop          Dollo and polymorphism parsimony algorithm
ffitch           Fitch-Margoliash and Least-Squares Distance Methods
fkitsch          Fitch-Margoliash method with contemporary tips
fneighbor        Phylogenies from distance matrix by N-J or UPGMA method
fmix             Mixed parsimony algorithm
fpars            Discrete character parsimony
fdnapars         DNA parsimony algorithm
fprotpars        Protein parsimony algorithm
fdnapenny        Penny algorithm for DNA
fdolpenny        Penny algorithm Dollo or polymorphism
fpenny           Penny algorithm, branch-and-bound
fseqboot         Bootstrapped sequences algorithm
fseqbootall      Bootstrapped sequences algorithm
ffreqboot        Bootstrapped genetic frequencies algorithm
frestboot        Bootstrapped restriction sites algorithm
fdiscboot        Bootstrapped discrete sites algorithm
frestdist        Distance matrix from restriction sites or fragments
ftreedist        Distances between trees
ftreedistpair    Distances between two sets of trees
fdrawgram        Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree        Plots an unrooted tree diagram
ffactor          Multistate to binary recoding program