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 | 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 |
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 pasimony algorithm |
frestboot | Bootstrapped restriction sites algorithm |
frestdist | 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 | Distances between trees |
ftreedistpair | Distances between two sets of trees |