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    phylip

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    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