PHYLOGENY:CONSENSUS
fconsense        Majority-rule and strict consensus tree
ftreedist        Distances between trees
ftreedistpair    Distances between two sets of trees

PHYLOGENY:CONTINUOUS CHARACTERS
fcontrast        Continuous character Contrasts

PHYLOGENY:DISCRETE CHARACTERS
fclique          Largest clique program
fdollop          Dollo and polymorphism parsimony algorithm
fdolpenny        Penny algorithm Dollo or polymorphism
ffactor          Multistate to binary recoding program
fmix             Mixed parsimony algorithm
fpars            Discrete character parsimony
fpenny           Penny algorithm, branch-and-bound

PHYLOGENY:DISTANCE MATRIX
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

PHYLOGENY:GENE FREQUENCIES
fcontml          Gene frequency and continuous character Maximum Likelihood
fgendist         Compute genetic distances from gene frequencies

PHYLOGENY:MOLECULAR SEQUENCE
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
fdnapars         DNA parsimony algorithm
fdnapenny        Penny algorithm for DNA
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

PHYLOGENY:TREE DRAWING
fdrawgram        Plots a cladogram- or phenogram-like rooted tree diagram
fdrawtree        Plots an unrooted tree diagram
