phytree

Data structure containing phylogenetic tree

Description

A phytree object is a data structure containing a phylogenetic tree. Phylogenetic trees are binary rooted trees, which means that each branch is the parent of two other branches, two leaves, or one branch and one leaf. A phytree object can be ultrametric or nonultrametric.

Creation

Syntax

tree = phytree(B)

tree = phytree(B,D)

tree = phytree(B,C)

tree = phytree(BC)

tree = phytree(___,N)

tree = phytree

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.

tree = phytree(B,D) creates an additive (ultrametric or nonultrametric) phylogenetic tree object with branch distances defined by D.

tree = phytree(B,C) creates an ultrametric phylogenetic tree object with distances between branches and leaves defined by 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, the branches, or both. Use this syntax with any of the previous arguments.

tree = phytree creates an empty phylogenetic tree object.

Input Arguments

B — Branches of the tree

numeric array of size [NUMBRANCHES X 2]

Branches of the tree, specified as a numeric array of size [NUMBRANCHES X 2]. Each row represents a branch of the tree. 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.

Data Types: double

D — Distances from every node to their parent branch

numeric array of size [NUMNODES X 1]

Distances from every node to their parent branch, specified as 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.

Data Types: double

C — Distances for every branch to leaves

numeric array of size [NUMBRANCHES X 1]

Distances for every branch to the leaves, specified as a numeric array of size [NUMBRANCHES X 1]. In ultrametric trees, all of the leaves are at the same location (same distance to the root).

Data Types: double

BC — Pointers to branches or leaves and distances of branches

matrix

Pointers to branches or leaves and distances of branches, specified as a combined matrix. The branch pointers are in BC(:,[1 2]) and branch coordinates are in BC(:,3).

The syntax phytree(BC) is the same as phytree(B,C).

Data Types: double

N — Names of leaves and branches

string vector | cell array of character vectors

Names of leaves and branches, specified as 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.

Data Types: string | cell

Properties

Note

You can access these properties using the get method.

NumLeaves — Number of leaves

positive integer

This property is read-only.

Number of leaves, stored as a positive integer.

NumBranches — Number of branches

positive integer

This property is read-only.

Number of branches, stored as a positive integer.

NumNodes — Number of nodes (NumLeaves + NumBranches)

positive integer

This property is read-only.

Number of nodes (NumLeaves + NumBranches), stored as a positive integer.

Pointers — Branch to leaf or branch connectivity list

matrix

This property is read-only.

Branch to leaf or branch connectivity list, stored as a matrix.

Distances — Edge length for every leaf or branch

numeric array of size [NUMNODES X 1]

This property is read-only.

Edge length for every leaf or branch, stored as a numeric array of size [NUMNODES X 1]. Here, NUMNODES = NUMLEAVES + NUMBRANCHES.

LeafNames — Names of the leaves

cell array of character vectors

This property is read-only.

Names of the leaves, stored as a cell array of character vectors.

BranchNames — Names of the branches

cell array of character vectors

This property is read-only.

Names of the branches, stored as a cell array of character vectors.

NodeNames — Names of all the nodes

cell array of character vectors

This property is read-only.

Names of all the nodes, stored as a cell array of character vectors.

Object Functions

cluster	Validate clusters in phylogenetic tree
get	Retrieve information about phylogenetic tree object
getbyname	Branches and leaves from phytree object
getcanonical	Calculate canonical form of phylogenetic tree
getmatrix	Convert phytree object into relationship matrix
getnewickstr	Create Newick-formatted character vector
pdist	Calculate pairwise patristic distances in phytree object
plot	Draw phylogenetic tree
prune	Remove branch nodes from phylogenetic tree
reorder	Reorder leaves of phylogenetic tree
reroot	Change root of phylogenetic tree
select	Select tree branches and leaves in phytree object
subtree	Extract phylogenetic subtree
view	View phylogenetic tree
weights	Calculate weights for phylogenetic tree

Examples

Ultrametric Phylogenetic Tree

Create a tree with three leaves and two branches.

B = [1 2;3 4];
tree = phytree(B)

    Phylogenetic tree object with 3 leaves (2 branches)

view(tree)

Additive Phylogenetic Tree

Create an additive (ultrametric or nonultrametric) phylogenetic tree object with branch distances specified as a column vector.

B = [1 2;3 4];
D = [1 2 1.5 1 0]';
tree = phytree(B,D);
view(tree)

Ultrametric Phylogenetic Tree with Specified Distances Between Branches and Leaves

Create an ultrametric phylogenetic tree object with distances between branches and leaves defined by a vector.

B = [1 2;3 4];
C = [1 4]';
tree = phytree(B,C)

    Phylogenetic tree object with 3 leaves (2 branches)

view (tree)

Phylogenetic Tree From File

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)

Version History

Introduced in R2006b