Added source Matlab code for reference

matlab/graph/@phyTree/Weights.m

@@ -0,0 +1,54 @@
+function W = weights(tr)
+%WEIGHTS Tree based sequence weights.
+%
+%  W = WEIGHTS(T) Calculates branch proportional weights for every leaf in
+%  the tree using the Thompson-Higgins-Gibson method. The distance of every
+%  segment of the tree is adjusted by dividing it by the number of leaves
+%  it contains. The sequence weights are the result of normalizing to the
+%  unity the new patristic distances between every leaf and the root.
+%
+%  Example:
+%
+%     % Create an ultrametric tree with specified branch distances
+%     bd = [1 2 3]';
+%     tr_1 = phytree([1 2;3 4;5 6],bd)
+%     view(tr_1) 
+%     weights(tr_1)
+%
+%  See also MULTIALIGN, PHYTREE, PROFALIGN, SEQLINKAGE.
+
+% References:
+%   J.D. Thompson, D.G. Higgins, and T.J. Gibson. Nucleic Acids Res. (1994)
+%   22(22):4673-4680.
+%   S.Henikoff and J. G. Henikoff. JMB. (1994) 243(4):574--578.
+%
+% Copyright 2003-2005 The MathWorks, Inc.
+% $Revision: 1.1.8.2 $Author: batserve $ $Date: 2005/06/17 20:19:24 $
+
+if numel(tr)~=1
+     error('Bioinfo:phytree:weights:NoMultielementArrays',...
+           'Phylogenetic tree must be an 1-by-1 object.');
+end
+
+numBranches = size(tr.tree,1);
+numLeaves = numBranches + 1;
+numLabels = numBranches + numLeaves; 
+
+% calculate the branch width
+branchWidth = ones(numLabels,1);
+for ind = 1:numBranches
+    branchWidth(numLeaves+ind) = sum(branchWidth(tr.tree(ind,:)));
+end 
+
+% adjust the distances
+tr.dist = tr.dist ./ branchWidth;
+
+% calculate distance of every leave to root
+cdist = tr.dist; 
+for ind = numBranches:-1:1
+    cdist(tr.tree(ind,:)) = cdist(tr.tree(ind,:)) + cdist(ind+numLeaves);
+end 
+
+W = cdist(1:numLeaves);
+W = W./max(W);
+