seqneighjoin

Construct phylogenetic tree using neighbor-joining method

Syntax

PhyloTree = seqneighjoin(Distances)

PhyloTree = seqneighjoin(Distances,Method)

PhyloTree = seqneighjoin(Distances,Method,Names)

PhyloTree = seqneighjoin(___,Reroot=RerootValue)

Description

PhyloTree = seqneighjoin(Distances) computes a phylogenetic tree object from pairwise distances between the species or products, using the neighbor-joining method.

PhyloTree = seqneighjoin(Distances,Method) specifies a method to compute the distances of the new nodes to all other nodes at every iteration. The general expression to calculate the distances between the new node, n, after joining i and j and all other nodes (k), is given by

D(n,k) =  a*D(i,k) + (1-a)*D(j,k) - a*D(n,i) - (1-a)*D(n,j)

This expression is guaranteed to find the correct tree with additive data (minimum variance reduction).

PhyloTree = seqneighjoin(Distances,Method,Names) passes a list of names (such as species or products), to label the leaf nodes in the phylogenetic tree object.

PhyloTree = seqneighjoin(___,Reroot=RerootValue) specifies whether to reroot PhyloTree. When PhyloTree is false, seqneighjoin excludes rerooting the resulting tree, which is useful for observing the original linkage order followed by the algorithm. By default seqneighjoin reroots the resulting tree using the midpoint method.

Examples

Build Phylogenetic Tree using Neighbor Joining Method

Create an array of structures representing a multiple alignment of amino acids:

seqs = fastaread('pf00002.fa');

Measure the Jukes-Cantor pairwise distances between sequences.

distances = seqpdist(seqs,'method','jukes-cantor','indels','pair');

Use the output argument distances, a vector containing biological distances between each pair of sequences, as an input argument to seqneighjoin.

Build the phylogenetic tree for the multiple sequence alignment using the neighbor-joining algorithm. Specify the method to compute the distances of the new nodes to all other nodes.

phylotree = seqneighjoin(distances,'equivar',seqs)

    Phylogenetic tree object with 32 leaves (31 branches)

View the phylogenetic tree:

view(phylotree)

Input Arguments

Distances — Biological distances between pairs of sequences

matrix | vector

Biological distances between pairs of sequences, specified as a matrix or vector, such as returned by the seqpdist function.

Data Types: double

Method — Method to compute the distances between nodes

"equivar" (default) | "firstorder"

Method to compute the distances between nodes, specified as "equivar" or "firstorder".

• "equivar" — Assumes equal variance and independence of evolutionary distance estimates (a = 1/2), such as in the original neighbor-joining algorithm by Saitou and Nei, JMBE (1987) or as in Studier and Keppler, JMBE (1988).

• "firstorder" — Assumes a first-order model of the variances and covariances of evolutionary distance estimates, with 'a' being adjusted at every iteration to a value between 0 and 1, such as in Gascuel, JMBE (1997).

Data Types: char | string

Names — List of names

vector of structures | cell array of character vectors | string vector

List of names, specified as one of these values:

• Vector of structures with the fields Header and Name

• Cell array of character vectors or string vector

The number of elements must equal the number of samples used to generate the pairwise distances in Distances.

Data Types: struct | string | cell

RerootValue — Control to reroot PhyloTree

true (default) | false

Control to reroot PhyloTree, specified as a true or false. When this value is false, seqneighjoin excludes rerooting the resulting tree, which is useful for observing the original linkage order followed by the algorithm. By default seqneighjoin reroots the resulting tree using the midpoint method.

Data Types: logical

Output Arguments

PhyloTree — Phylogenetic tree

phytree object

Biological distances between pairs of sequences, returned as a phytree object.

References

[1] Saitou, N., and M. Nei. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4) (1987): 406–425.

[2] Gascuel, O. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution 14 (1997): 685–695.

[3] Studier, J.A., and K.J. Keppler. A note on the neighbor-joining algorithm of Saitou and Nei. Molecular Biology and Evolution 5(6) (1988): 729–731.

Version History

Introduced before R2006a