PHYLIPNEW Applications
The PHYLIPNEW programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.61 (August 2004).
The PHYLIPNEW versions of these programs all have the prefix "f" to distinguish them from the original programs.
Applications in the current phylipnew release
| 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 parsimony 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 |