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    phylip

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    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 ]

    v3.6
    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