phylip

This file has been automatically converted from the original documentation for easy use inside the ARB help system. Differences compared with the original documentation are unintentionally caused by the conversion process. In doubt please refer to the original documentation!

[ generated from ../../GDE/PHYLIP/phylip.html ]

PHYLIP, the PHYLogeny Inference Package, consists of 34 programs. There are documentation files for each program, in the form of web pages in HTML 3.2. There are also documentation web pages for each group of programs, and a main documentation file that is the basic introduction to the package. Before running any of the programs you should read it.

Below you will find a list of the programs and the documentation files. The names of the documentation files are highlighted as links that will take you to those documentation files.

         molecular sequence programs documentation file
protpars protein parsimony documentation file
dnapars  DNA sequence parsimony documentation file
dnapenny DNA parsimony branch and bound documentation file
dnamove  interactive DNA parsimony documentation file
dnacomp  DNA compatibility documentation file
dnaml    DNA maximum likelihood documentation file
dnamlk   DNA maximum likelihood with clock documentation file
proml    Protein sequence maximum likelihood documentation file
promlk   Protein sequence maximum likelihood with clock documentation
         file
dnainvar DNA invariants documentation file
dnadist  DNA distance documentation file
protdist Protein sequence distance documentation file
restdist Restriction sites and fragments distances documentation file
seqboot  Bootstrapping/Jackknifing documentation file

         Distance matrix programs documentation file
fitch    Fitch-Margoliash distance matrix method documentation file
kitsch   Fitch-Margoliash distance matrix with clock documentation file
neighbor Neighbor-Joining and UPGMA method documentation file

         Continuous characters and gene frequencies documentation file
contml   Maximum likelihood continuous characters and gene frequencies
         documentation file
contrast Contrast method documentation file
gendist  Genetic distance documentation file

         Discrete characters methods documentation file
pars     Unordered multistate parsimony documentation file
mix      Mixed method parsimony documentation file
penny    Branch and bound mixed method parsimony documentation file
move     Interactive mixed method parsimony documentation file
dollop   Dollo and polymorphism parsimony documentation file
dolpenny Dollo and polymorphism branch and bound parsimony
         documentation file
dolmove  Dollo and polymorphism interactive parsimony documentation file
clique   0/1 characters compatibility method documentation file
factor   Character recoding program documentation file

         Tree drawing programs documentation file
drawgram Rooted tree drawing program documentation file
drawtree Unrooted tree drawing program documentation file

consense Consensus tree program documentation file
treedist Tree distance program documentation file
retree   interactive tree rearrangement program documentation file