FITCH -- Fitch-Margoliash and Least-Squares Distance Methods
version 3.5c
CONTENTS:
(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.
DESCRIPTION
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
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Maintained 15 Jul 1996 -- by Martin Hilbers(e-mail:M.P.Hilbers@dl.ac.uk)