Create phytree object
Tree = phytree(B)
Tree = phytree(B, D)
Tree = phytree(B, C)
Tree = phytree(BC)
Tree = phytree(..., N)
Tree = phytree
|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.|
|Cell array with the names of leaves and branches.|
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 cell of strings. 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.
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.
cluster | get | getbyname | getcanonical | getmatrix | getnewickstr | pdist | phytreeread | phytreeviewer | phytreewrite | plot | prune | reroot | select | seqlinkage | seqneighjoin | seqpdist | subtree | view | weights