EMBOSS: PHYLIP

| ## EMBOSS: PHYLIP

# Original PHYLIP fitch 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

             FITCH -- Fitch-Margoliash and Least-Squares Distance Methods

    (c) Copyright  1986-1993  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 carries out Fitch-Margoliash, Least Squares, and a number  of
    similar methods as described in the documentation file for distance methods.

         The options for FITCH are selected through  the  menu,  which  looks  like
    this:

    Fitch-Margoliash method version 3.5c

    Settings for this run:
      U                 Search for best tree?  Yes
      P                                Power?  2.00000
      -      Negative branch lengths allowed?  No
      O                        Outgroup root?  No, use as outgroup species  1
      L         Lower-triangular data matrix?  No
      R         Upper-triangular data matrix?  No
      S                        Subreplicates?  No
      G                Global rearrangements?  No
      J     Randomize input order of species?  No. Use input order
      M           Analyze multiple data sets?  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
      3                        Print out tree  Yes
      4       Write out trees onto tree file?  Yes

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

    Most of the input options (U, P, -, O, L, R, S, J, and M) are as given in  that
    file,  and  their  input  format is the same as given there.  The U (User Tree)
    option has one additional feature when the N (Lengths) option  is  used.   This
    menu  option  will  appear  only if the U (User Tree) option is selected.  If N
    (Lengths) is set to "Yes" then if any branch in the  user  tree  has  a  branch
    length,  that  branch  will not have its length iterated.  Thus you can prevent
    all branches from having their lengths changed by giving them  all  lengths  in
    the  user  tree, or hold only one length unchanged by giving only that branch a
    length (such as, for example, 0.00).  You may find program  RETREE  useful  for
    adding  and  removing branch lengths from a tree.  This option can also be used
    to compute the Average Percent Standard Deviation  for  a  tree  obtained  from
    NEIGHBOR, for comparison with trees obtained by FITCH or KITSCH.

         Another input option available in FITCH that is not available in KITSCH or
    NEIGHBOR  is  the  G  (Global)  option.   G  is the Global search option.  This
    causes, after the last species is added to the tree, each possible group to  be
    removed  and  re-added.   This improves the result, since the position of every
    species is reconsidered.  It approximately triples the run-time of the program.
    It  is not an option in KITSCH because it is the default and is always in force
    there.  The O (Outgroup) option is described in the main documentation file  of
    this  package.   The  O option has no effect if the tree is a user-defined tree
    (if the U option is in effect).  The U (User Tree) option requires an  unrooted
    tree; that is, it require that the tree have a trifurcation at its base:

         ((A,B),C,(D,E));

         The output consists of an unrooted tree and the lengths  of  the  interior
    segments.   The  sum  of  squares  is  printed  out,  and  if P = 2.0 Fitch and
    Margoliash's "average percent standard deviation" is also computed and  printed
    out.   This  is  the sum of squares, divided by N-2, and then square-rooted and
    then multiplied by 100 (n is the number of species on the tree):

                              1/2
         APSD = ( SSQ / (N-2) )    x 100.

    where N is the total number of off-diagonal distance measurements that  are  in
    the  (square) distance matrix.  If the S (subreplication) option is in force it
    is instead the sum of the numbers of replicates in all the  non-diagonal  cells
    of  the  distance  matrix.  But if the L or R option is also in effect, so that
    the distance matrix read in is lower- or  upper-triangular,  then  the  sum  of
    replicates  is  only  over those cells actually read in.  If S is not in force,
    the number of replicates in each cell is assumed to be 1, so that N is  n(n-1),
    where  n is the number of species.  The APSD gives an indication of the average
    percentage error.  The number of trees examined is also printed out.

         The constants available for modification at the beginning of  the  program
    are: "smoothings", which gives the number of passes through the algorithm which
    adjusts the lengths of the segments of the tree so as to minimize  the  sum  of
    squares, "namelength", which gives the length of a species name, and "epsilon",
    which defines a small quantity needed in some of the calculations.  There is no
    feature  saving  multiply  trees tied for best, partly because we do not expect
    exact ties except in cases where the branch lengths make the nature of the  tie
    obvious, as when a branch is of zero length.

         The algorithm can be slow.  As the number of species rises,  so  does  the
    number  of  distances  from  each  species  to  the  others.  The speed of this
    algorithm will thus rise as the fourth power of the number of  species,  rather
    than  as the third power as do most of the others.  Hence it is expected to get
    very slow as the number of species is made larger.

    -----------------------------TEST DATA SET------------------------------

        5
    Alpha      0.000 1.000 2.000 3.000 3.000
    Beta       1.000 0.000 2.000 3.000 3.000
    Gamma      2.000 2.000 0.000 3.000 3.000
    Delta      3.000 3.000 3.000 0.000 1.000
    Epsilon    3.000 3.000 3.000 1.000 0.000

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

       5 Populations

    Fitch-Margoliash method version 3.5c

                      __ __             2
                           (Obs - Exp)
    Sum of squares =  /_ /_  ------------
                                    2
                       i  j      Obs

    Negative branch lengths not allowed

    Name                       Distances
    ----                       ---------

    Alpha         0.00000   1.00000   2.00000   3.00000   3.00000
    Beta          1.00000   0.00000   2.00000   3.00000   3.00000
    Gamma         2.00000   2.00000   0.00000   3.00000   3.00000
    Delta         3.00000   3.00000   3.00000   0.00000   1.00000
    Epsilon       3.00000   3.00000   3.00000   1.00000   0.00000

      +---------Beta
      !
      !                                       +---------Epsilon
      !         +-----------------------------3
    --1---------2                             +---------Delta
      !         !
      !         +-------------------Gamma
      !
      +---------Alpha

    remember: this is an unrooted tree!

    Sum of squares =     0.00000

    Average percent standard deviation =     0.00000

    examined   15 trees

    Between        And            Length
    -------        ---            ------
       1          Beta              0.50000
       1             2              0.50000
       2             3              1.50000
       3          Epsilon           0.50000
       3          Delta             0.50000
       2          Gamma             1.00000
       1          Alpha             0.50000