| Bioinformatics Toolbox | |
Construct phylogenetic tree from pairwise distances
Tree = seqlinkage(Dist) Tree = seqlinkage(Dist, Method) Tree = seqlinkage(Dist, Method, Names)
Dist | Pairwise distances generated from the function seqpdist. |
Method | Property to select a distance method. Enter a method from the table below. |
Names | Property to use alternative labels for leaf nodes. Enter a vector of structures, with the fields 'Header' or 'Name', or a cell array of strings. In both cases the number of elements you provide must comply with the number of samples used to generate the pairwise distances in Dist. |
Tree = seqlinkage(Dist) returns a phylogenetic tree object from the pairwise distances (Dist) between the species or products. Dist is a matrix (or vector) such as is generated by the function seqpdist.
Tree = seqlinkage(Dist, Method) creates a phylogenetic tree object using a specified patristic distance method. The available methods are
'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) |
Tree = seqlinkage(Dist, Method, Names) passes a list of names to label the leaf nodes (for example, species or products) in a phylogenetic tree object.
% Load a multiple alignment of amino acids:
seqs = fastaread('pf00002.fa');
% Measure the 'Jukes-Cantor' pairwise distances:
dist = seqpdist(seqs,'method','jukes-cantor',...
'indels','pair');
% Build the phylogenetic tree with the single linkage
% method and pass the names of the sequences:
tree = seqlinkage(dist,'single',seqs)
view(tree)
The Bioinformatics Toolbox functions phytree (phytree), phytreewrite, seqpdist
phytree object methods plot and view
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