| ## EMBOSS: PHYLIP

# Original PHYLIP contrast documentation.

This is the original PHYLIP documentation and includes information on the old menu driven program which is now replaced with the EMBOSS acd file.

                                                                       version 3.5c

                 CONTRAST -- Computes contrasts for comparative method

    (c) Copyright  1991-1993  by  Joseph  Felsenstein  and  by  the  University  of
    Washington.  Written by Joseph Felsenstein.  Permission is granted to copy this
    document provided that no fee is charged for it and that this copyright  notice
    is not removed.

         This program implements the contrasts calculation  described  in  my  1985
    paper  on  the comparative method (Felsenstein, 1985d).  It reads in a data set
    of the standard  quantitative  characters  sort,  and  also  a  tree  from  the
    treefile.   It then forms the contrasts between species that, according to that
    tree, are statistically independent.  This is done  for  each  character.   The
    contrasts  are  all  standardized  by branch lengths (actually, square roots of
    branch lengths).

         The method is explained in the 1985 paper.  It assumes a  Brownian  motion
    model.   This  model  was  introduced  by  Edwards  and  Cavalli-Sforza  (1964;
    Cavalli-Sforza and Edwards, 1967) as an approximation to the evolution of  gene
    frequencies.   I  have  discussed (Felsenstein, 1973b, 1981c, 1985d, 1988b) the
    difficulties inherent in using it as a model for the evolution of  quantitative
    characters.  Chief among these is that the characters do not necessarily evolve
    independently or at equal rates.  This program allows one to evaluate this,  if
    there  is  independent  information  on  the  phylogeny.   You  can compute the
    variance of the contrasts for each character, as  a  measure  of  the  variance
    accumulating  per  unit  branch  length.   You  can  also  test  covariances of
    characters.

         The input file is as described in the continuous characters  documentation
    file  above,  for  the  case  of  continuous  quantitative characters (not gene
    frequencies).  Options are selected using a menu:

    Continuous character Contrasts, version 3.5c

    Settings for this run:
      R     Print out correlations and regressions?  Yes
      M                     Analyze multiple trees?  No
      0         Terminal type (IBM PC, VT52, ANSI)?  ANSI
      1          Print out the data at start of run  No
      2        Print indications of progress of run  Yes

    Are these settings correct? (type Y or the letter for one to change)

    M is similar to the usual multiple data sets input option, but is used here  to
    allow multiple trees to be read from the treefile, not multiple data sets to be
    read from the input file.  In this way you can use bootstrapping  on  the  data
    that  estimated  these trees, get multiple bootstrap estimates of the tree, and
    then use the M option to make  multiple  analyses  of  the  contrasts  and  the
    covariances,  correlations,  and regressions.  In this way (Felsenstein, 1988b)
    you can assess the effect of the inaccuracy of the trees on your  estimates  of
    these statistics.

    R allows you to turn off or on the printing out of the statistics.   If  it  is
    off only the contrasts will be printed out (unless option 1 is selected).  With
    only the contrasts printed out, they are in a simple array that is  in  a  form
    that  many statistics packages should be able to read.  The contrasts are rows,
    and each row has one contrast for each character.  Any multivariate  statistics
    package  should  be  able to analyze these (but keep in mind that the contrasts
    have, by virtue of the  way  they  are  generated,  expectation  zero,  so  all
    regressions must pass through the origin).

         The tree file should contain the desired tree  or  trees.   These  can  be
    either  in  bifurcating form, or may have the bottommost fork be a trifurcation
    (it should not matter which of these ways you  present  the  tree).   The  tree
    must, of course, have branch lengths.

         If you have a molecular data set (for  example)  and  also,  on  the  same
    species,  quantitative  measurements,  here  is  how  you  can  allow  for  the
    uncertainty of yor estimate of the tree.  Use SEQBOOT to generate multiple data
    sets  from  your  molecular data.  Then, whichever method you use to analyze it
    (the relevant ones are those that produce  estimates  of  the  branch  lengths:
    DNAML,  DNAMLK,  FITCH, KITSCH, and NEIGHBOR -- the latter three require you to
    use DNADIST to turn the bootstrap data sets into multiple  distance  matrices),
    you should use the Multiple Data Sets option of that program.  This will result
    in a tree file with many trees on it.  Then use this tree file with  the  input
    file  containing your continuous quantitative characters, choosing the Multiple
    Trees (M) option.  You will get one set of contrasts and  statistics  for  each
    tree  in  the  tree  file.  At the moment there is no overall summary: you will
    have to tabulate these by hand.  A similar process can be followed if you  have
    restriction sites data (using RESTML) or gene frequencies data.

         The statistics that are printed out include the  covariances  between  all
    pairs  of characters, the regressions of each character on each other (column j
    is regressed on row i), and the correlations between all pairs  of  characters.
    In  assessing  degress of freedom it is important to realize that each contrast
    was taken to have expectation zero, which is known because each contrast  could
    as  easily have been computed xi-xj instead of xj-xi.  Thus there is no loss of
    a degree of freedom for estimation of a mean.  The degrees of freedom  is  thus
    the same as the number of contrasts, namely one less than the number of species
    (tips).  If you feed these contrasts into  a  multivariate  statistics  program
    make sure that it knows that each variable has expectation exactly zero.

         A limitation of these programs is that they use  species  means  for  each
    quantitative  character without attempting to correct for the finiteness of the
    sample size in the estimation of this mean.  Thus the  variability  taken  into
    account  in  the  model  is  randomness  of change in evolution, but not random
    sampling in the estimation of the species means.  I hope to remedy this in  the
    future.   At  the  moment  I  do not have a good method of inputting individual
    measurements, just species means.  Another  limitation  is  the  absence  of  a
    method for indicating missing data.  The current program assumes all characters
    have been measured in all species.

         The constants available for modification at the beginning of  the  program
    include the usual boolean contants for the terminal type plus "namelength", the
    length of species names.

         The data set used as an example below is  the  example  from  a  paper  by
    Michael Lynch (1990), his characters having been log-transformed.

    --------------------- TEST SET INPUT ------------------------------------

        5   2
    Homo        4.09434  4.74493
    Pongo       3.61092  3.33220
    Macaca      2.37024  3.36730
    Ateles      2.02815  2.89037
    Galago     -1.46968  2.30259

    --------------------- TEST SET INPUT TREEFILE ---------------------------

    ((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);

    --------------- TEST SET OUTPUT (with all numerical options on ) -------------

    Continuous character Contrasts, version 3.5c

       5 Populations,    2 Characters

    Name                       Phenotypes
    ----                       ----------

    Homo         4.09434   4.74493
    Pongo        3.61092   3.33220
    Macaca       2.37024   3.36730
    Ateles       2.02815   2.89037
    Galago      -1.46968   2.30259

    Contrasts (columns are different characters)
    --------- -------- --- --------- -----------

       0.74593   2.17989
       1.58474   0.71761
       1.19293   0.86790
       3.35832   0.89706

    Covariance matrix
    ---------- ------

        3.9423    1.7028
        1.7028    1.7062

    Regressions (columns on rows)
    ----------- -------- -- -----

        1.0000    0.4319
        0.9980    1.0000

    Correlations
    ------------

        1.0000    0.6566
        0.6566    1.0000