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# phylip

- DISCLAIMER
- DOCUMENTATION

## DISCLAIMER

### 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!

## DOCUMENTATION

    # generated from ../../GDE/PHYLIP/phylip.html
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PHYLIP programs and documentation
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.
Introduction to PHYLIP
main documentation file
Molecular sequence methods
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 methods

             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

Gene frequencies and continuous characters
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
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, consensus, tree editing, tree distances

             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