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weights (phytree)

Calculate weights for phylogenetic tree

Syntax

W = weights(Tree)

Arguments

Tree

Phylogenetic tree (phytree object) created with the function phytree.

Description

W = weights(Tree) calculates branch proportional weights for every leaf in a tree (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 unity the new patristic distances between every leaf and the root.

Examples

  1. Create an ultrametric tree with specified branch distances.

    bd = [1 2 3]';
    tr_1 = phytree([1 2;3 4;5 6],bd)
  2. View the tree.

    view(tr_1)

  3. Display the calculated weights.

    weights(tr_1)
    
    ans =
    
        1.0000
        1.0000
        0.8000
        0.8000

References

[1] Thompson JD, Higgins DG, Gibson TJ (1994), "CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice," Nucleic Acids Research, 22(22):4673-4680.

[2] Henikoff S, Henikoff JG (1994), “Position-based sequence weights,” Journal Molecular Biology, 243(4):574-578.

Introduced before R2006a