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