Phylip PHYLogeny Inference Package Version 3.5c Go to the PHYLIP Main Page in Washington You can search the indexed Phylip manuals: Indexed Phylip Manuals You can read a general description of Phylip here: Phylip Manual Phylip consists of the following modules: Programs for molecular sequence data PROTPARS Protein parsimony DNAPARS Parsimony method for DNA DNAMOVE Interactive DNA parsimony DNAPENNY Branch and bound for DNA DNACOMP Compatibility for DNA DNAINVAR Phylogenetic invariants DNAML Maximum likelihood method DNAMLK DNA ML with molecular clock DNADIST Distances from sequences PROTDIST Distances from proteins RESTML ML for restriction sites SEQBOOT Bootstraps sequence data sets COALLIKE Coalescent likelihoods from sampled phylogeny estimates Programs for distance matrix data FITCH Fitch-Margoliash and least-squares methods KITSCH Fitch-Margoliash and least squares methods with evolutionary clock NEIGHBOR Neighbor-joining and UPGMA methods Programs for gene frequencies and continuous characters CONTML Maximum likelihood method GENDIST Computes genetic distances CONTRAST Computes contrasts and correlations for comparative method studies Programs for 0-1 discrete state data MIX Wagner, Camin-Sokal, and mixed parsimony criteria MOVE Interactive Wagner, C-S, mixed parsimony program PENNY Finds all most parsimonious trees by branch-and-bound DOLLOP, DOLMOVE, DOLPENNY same as preceding four programs, but for the Dollo and polymorphism parsimony criteria CLIQUE Compatibility method FACTOR recode multistate characters Programs for plotting trees and consensus trees DRAWGRAM Draws cladograms and phenograms on screens, plotters and printers DRAWTREE Draws unrooted phylogenies on screens, plotters and printers CONSENSE Majority-rule and strict consensus trees RETREE Reroots, changes names and branch lengths, and flips trees There is also an Unsupported Division containing two programs, makeinf and