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    fitch.doc

    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/doc/fitch.html

    version 3.6
    FITCH -- Fitch-Margoliash and Least-Squares Distance Methods
    (C)  Copyright  1986-2002  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 3.6a3

    Settings for this run:
      D      Method (F-M, Minimum Evolution)?  Fitch-Margoliash
      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, ANSI, none)?  (none)
      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
    Y to accept these or type the letter for one to change
    Most of the input options (U, P, -, O, L, R, S, J, and M) are as given
    in  the  documentation  page  for  distance matrix programs, 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.
    The  D  (methods)  option  allows  choice between the Fitch-Margoliash
    criterion and the Minimum Evolution method (Kidd and Sgaramella-Zonta,
    1971;  Rzhetsky  and Nei, 1993). Minimum Evolution (not to be confused
    with  parsimony)  uses  the  Fitch-Margoliash  criterion to fit branch
    lengths  to  each topology, but then chooses topologies based on their
    total  branch length (rather than the goodness of fit sum of squares).
    There  is  no  constraint  on  negative  branch lengths in the Minimum
    Evolution method; it sometimes gives rather strange results, as it can
    like  solutions  that  have  large  negative  branch lengths, as these
    reduce the total sum of branch lengths!
    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):
    APSD = ( SSQ / (N-2) )^1/2 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, "delta", which controls the size of
    improvement  in  sum  of squares that is used to control the number of
    iterations  improving  branch lengths, and "epsilonf", 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
        7
    Bovine      0.0000  1.6866  1.7198  1.6606  1.5243  1.6043  1.5905
    Mouse       1.6866  0.0000  1.5232  1.4841  1.4465  1.4389  1.4629
    Gibbon      1.7198  1.5232  0.0000  0.7115  0.5958  0.6179  0.5583
    Orang       1.6606  1.4841  0.7115  0.0000  0.4631  0.5061  0.4710
    Gorilla     1.5243  1.4465  0.5958  0.4631  0.0000  0.3484  0.3083
    Chimp       1.6043  1.4389  0.6179  0.5061  0.3484  0.0000  0.2692
    Human       1.5905  1.4629  0.5583  0.4710  0.3083  0.2692  0.0000
         _________________________________________________________________
    OUTPUT FROM TEST DATA SET (with all numerical options on)
    7 Populations

    Fitch-Margoliash method version 3.6a3

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

    Negative branch lengths not allowed

    Name                       Distances
    ----                       ---------
    Bovine        0.00000   1.68660   1.71980   1.66060   1.52430   1.60430
                  1.59050
    Mouse         1.68660   0.00000   1.52320   1.48410   1.44650   1.43890
                  1.46290
    Gibbon        1.71980   1.52320   0.00000   0.71150   0.59580   0.61790
                  0.55830
    Orang         1.66060   1.48410   0.71150   0.00000   0.46310   0.50610
                  0.47100
    Gorilla       1.52430   1.44650   0.59580   0.46310   0.00000   0.34840
                  0.30830
    Chimp         1.60430   1.43890   0.61790   0.50610   0.34840   0.00000
                  0.26920
    Human         1.59050   1.46290   0.55830   0.47100   0.30830   0.26920
                  0.00000
    +---------------------------------------------Mouse
    !
    !                                +------Human
    !                             +--5
    !                           +-4  +--------Chimp
    !                           ! !
    !                        +--3 +---------Gorilla
    !                        !  !
    1------------------------2  +-----------------Orang
    !                        !
    !                        +---------------------Gibbon
    !
    +------------------------------------------------------Bovine

    remember: this is an unrooted tree!

    Sum of squares =     0.01375
    Average percent standard deviation =     1.85418
    Between        And            Length
    -------        ---            ------
       1          Mouse             0.76985
       1             2              0.41983
       2             3              0.04986
       3             4              0.02121
       4             5              0.03695
       5          Human             0.11449
       5          Chimp             0.15471
       4          Gorilla           0.15680
       3          Orang             0.29209
       2          Gibbon            0.35537
       1          Bovine            0.91675