seqlinkage

Construct phylogenetic tree from pairwise distances

Syntax

PhyloTree = seqlinkage(Distances)

PhyloTree = seqlinkage(Distances, Method)

PhyloTree = seqlinkage(Distances, Method, Names)

Description

PhyloTree = seqlinkage(Distances) returns a phylogenetic tree object from the pairwise distances, Distances, between the species or products. Distances is a matrix or vector of pairwise distances, such as returned by the seqpdist function.

PhyloTree = seqlinkage(Distances, Method) creates a phylogenetic tree object using a specified patristic distance method.

PhyloTree = seqlinkage(Distances, Method, Names) passes a list of unique names to label the leaf nodes (for example, species or products) in a phylogenetic tree object.

Examples

Build Phylogenetic Tree from Pairwise Distances

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');

Build the phylogenetic tree for the multiple sequence alignment from calculated pairwise distances. Specify the method to compute the distances of the new nodes to all other nodes. Provide leaf names:

phylotree = seqlinkage(distances,'single',seqs)

    Phylogenetic tree object with 32 leaves (31 branches)

View the phylogenetic tree:

view(phylotree)

Input Arguments

Distances — Matrix or vector of pairwise distances

matrix | vector

Matrix or vector of pairwise distances, such as returned by the seqpdist function.

Method — Character vector or string that specifies a distance method

character vector | string

Character vector or string that specifies a distance method. Choices are:

• 'single'

• 'complete'

• 'average' (default)

• 'weighted'

• 'centroid'

• 'median'

'single'	Nearest distance (single linkage method)
'complete'	Furthest distance (complete linkage method)
'average' (default)	Unweighted Pair Group Method Average (UPGMA, group average).
'weighted'	Weighted Pair Group Method Average (WPGMA)
'centroid'	Unweighted Pair Group Method Centroid (UPGMC)
'median'	Weighted Pair Group Method Centroid (WPGMC)

Names — Specifies alternative labels for leaf nodes

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

Specifies alternative labels for leaf nodes. Choices are:

• Vector of structures, each with a Header or Name field

• Cell array of character vectors or string vector

The elements must be unique. The number of elements must comply with the number of samples used to generate the pairwise distances in Dist.

Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64 | logical | char | string | struct | table | cell | function_handle | categorical | datetime | duration | calendarDuration | fi
Complex Number Support: Yes

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: phylotree = seqlinkage(distances,'single',seqs)

Method — Specifies the distance method

average (default) | single | complete

Character vector or string that specifies a distance method..

Example: phylotree = seqlinkage(distances,'single',seqs)

Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64 | logical | char | string | struct | table | cell | function_handle | categorical | datetime | duration | calendarDuration | fi
Complex Number Support: Yes

Version History

Introduced before R2006a

R2017b: seqlinkage correctly computes the input pairwise distances

For the R2017a or earlier versions, seqlinkage incorrectly doubled the input pairwise distances when building a tree. This bug has been fixed in R2017b.

If you have been previously selecting a subset of the tree returned by seqlinkage with a distance threshold, consider dividing the threshold by 2.

Note that the tree topology has always been computed correctly and not affected by this bug.