# PHYLIPNEW Applications

The PHYLIPNEW programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.69.

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 | 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