phytree

Create phytree object

Syntax

Tree = phytree(B)
Tree = phytree(B, D)
Tree = phytree(B, C)
Tree = phytree(BC)
Tree = phytree(..., N)
Tree = phytree


Arguments

B	Numeric array of size [NUMBRANCHES X 2] in which every row represents a branch of the tree. It contains two pointers to the branch or leaf nodes, which are its children.
C	Column vector with distances for every branch.
D	Column vector with distances from every node to their parent branch.
BC	Combined matrix with pointers to branches or leaves, and distances of branches.
N	Cell array with the names of leaves and branches.

Description

Tree = phytree(B) creates an ultrametric phylogenetic tree object. In an ultrametric phylogenetic tree object, all leaves are the same distance from the root.

B is a numeric array of size [NUMBRANCHES X 2] in which every row represents a branch of the tree and it contains two pointers to the branch or leaf nodes, which are its children.

Leaf nodes are numbered from 1 to NUMLEAVES and branch nodes are numbered from NUMLEAVES + 1 to NUMLEAVES + NUMBRANCHES. Note that because only binary trees are allowed, NUMLEAVES = NUMBRANCHES + 1.

Branches are defined in chronological order (for example, B(i,:) > NUMLEAVES + i). As a consequence, the first row can only have pointers to leaves, and the last row must represent the root branch. Parent-child distances are set to 1, unless the child is a leaf and to satisfy the ultrametric condition of the tree its distance is increased.

Given a tree with three leaves and two branches as an example.

In the MATLAB^® Command Window, type

B = [1 2 ; 3 4]

 B =

     1     2
     3     4

tree = phytree(B)

 Phylogenetic tree object with 3 leaves (2 branches)

view(tree)

Tree = phytree(B, D) creates an additive (ultrametric or nonultrametric) phylogenetic tree object with branch distances defined by D. D is a numeric array of size [NUMNODES X 1] with the distances of every child node (leaf or branch) to its parent branch equal to NUMNODES = NUMLEAVES + NUMBRANCHES. The last distance in D is the distance of the root node and is meaningless.

b = [1 2 ; 3 4 ]

b =

     1     2
     3     4

d = [1; 2; 1.5; 1; 0]

d =

    1.0000
    2.0000
    1.5000
    1.0000
         0

view(phytree(b,d))

Tree = phytree(B, C) creates an ultrametric phylogenetic tree object with distances between branches and leaves defined by C. C is a numeric array of size [NUMBRANCHES X 1], which contains the distance from each branch to the leaves. In ultrametric trees, all of the leaves are at the same location (same distance to the root).

b = [1 2 ; 3 4]

b =

     1     2
     3     4

c = [1 4]'

c =

     1
     4

view(phytree(b,c))

Tree = phytree(BC) creates an ultrametric phylogenetic binary tree object with branch pointers in BC(:,[1 2]) and branch coordinates in BC(:,3). Same as phytree(B,C).

Tree = phytree(..., N) specifies the names for the leaves and/or the branches. N is a string vector or cell array of character vectors. If NUMEL(N)==NUMLEAVES, then the names are assigned chronologically to the leaves. If NUMEL(N)==NUMBRANCHES, the names are assigned to the branch nodes. If NUMEL(N)==NUMLEAVES + NUMBRANCHES, all the nodes are named. Unassigned names default to 'Leaf #' and/or 'Branch #' as required.

Tree = phytree creates an empty phylogenetic tree object.

Examples

Create a Phylogenetic Tree

This example shows how to create a phylogenetic tree from a multiple sequence alignment file.

Read a multiple sequence alignment file.

Sequences = multialignread('aagag.aln');

Calculate the distance between each pair of sequences.

distances = seqpdist(Sequences);

Construct a phylogenetic tree object from the pairwise distances calculated previously.

tree = seqlinkage(distances);

View the phylogenetic tree.

phytreeviewer(tree)