PHYLIP Documents*

WARNING: Under construction
"HTMLized" by Jun ISHIKAWA <jun@nih.go.jp>
Last modified: Fri Apr 18 13:40:08 1997


Main document
Sequence format
Programs for molecular sequence data
DNAPARSParsimony method for DNA PROTPARSProtein parsimony
DNAMOVEInteractive DNA parsimony DNAPENNYBranch and bound for DNA
DNACOMPCompatibility for DNA DNAINVARPhylogenetic invariants
DNAMLMaximum likelihood method DNAMLKDNA ML with molecular clock
DNADISTDistances from sequences PROTDISTDistances from proteins
RESTMLML for restriction sites SEQBOOTBootstraps sequence data sets
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
Programs in the Unsupported Division
MAKEINF MAKE INFile

* PHYLIP (Version 3.57c) documents has been written by Joseph Felsenstein. Original copyright notice is as follow:

(c) Copyright 1986-1995 by Joseph Felsenstein and the University of Washington. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.