© Copyright 19862008 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 FitchMargoliash, 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:
FitchMargoliash method version 3.69 Settings for this run: D Method (FM, Minimum Evolution)? FitchMargoliash 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 Lowertriangular data matrix? No R Uppertriangular 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)? 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 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 FitchMargoliash criterion and the Minimum Evolution method (Kidd and SgaramellaZonta, 1971; Rzhetsky and Nei, 1993). Minimum Evolution (not to be confused with parsimony) uses the FitchMargoliash 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 readded. This improves the result, since the position of every species is reconsidered. It approximately triples the runtime 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 userdefined tree (if the U option is in effect). The U (User Tree) option requires an unrooted tree; that is, it requires 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 N2, and then squarerooted and then multiplied by 100:
APSD = ( SSQ / (N2) )^{1/2} x 100.
where N is the total number of offdiagonal 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 nondiagonal 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 uppertriangular, 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(n1), 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 multiple 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.
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 
7 Populations FitchMargoliash method version 3.69 __ __ 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 ! ! ! 12 +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 