Bioinformatics Toolbox™

getcanonical (phytree) - Calculate canonical form of phylogenetic tree

Syntax

Pointers = getcanonical(Tree)
[Pointers, Distances, Names] = getcanonical(Tree)

Arguments

Description

Pointers = getcanonical(Tree) returns the pointers for the canonical form of a phylogenetic tree (Tree). In a canonical tree the leaves are ordered alphabetically and the branches are ordered first by their width and then alphabetically by their first element. A canonical tree is isomorphic to all the trees with the same skeleton independently of the order of their leaves and branches.

[Pointers, Distances, Names] = getcanonical(Tree) returns, in addition to the pointers described above, the reordered distances (Distances) and node names (Names).

Examples

1. Create two phylogenetic trees with the same skeleton but slightly different distances.

   b = [1 2; 3 4; 5 6; 7 8;9 10];
   tr_1 = phytree(b,[.1 .2 .3 .3 .4 ]');
   tr_2 = phytree(b,[.2 .1 .2 .3 .4 ]');

2. Plot the trees.

    plot(tr_1)
    plot(tr_2)

3. Check whether the trees have an isomorphic construction.

   isequal(getcanonical(tr_1),getcanonical(tr_2))  
   
   ans =
        1

See Also

Bioinformatics Toolbox functions: phytree (object constructor), phytreeread

Bioinformatics Toolbox methods of phytree object: getbyname, select, subtree

getbyname (phytree)

getdescendants (biograph)