| Bioinformatics Toolbox | |
Functions for phylogenetic tree building and analysis.
Phylogenetic tree data — Read and write Newick formatted tree files (phytreeread, phytreewrite) into the MATLAB workspace as phylogenetic tree objects (phytree).
Create a phylogenetic tree — Calculate the pairwise distance between biological sequences (seqpdist), construct a phylogenetic tree from pairwise distances (seqlinkage), and view the tree in an interactive GUI that allows you to view, edit, and explore the data (phytreetool or view). This GUI also allows you to prune branches, reorder, rename, and explore distances.
Phylogenetic tree object methods — You can access the functionality of the phytreetool GUI using methods (functions) for a phylogenetic tree object (phytree). Get property values (get) and node names (getbyname). Calculate the patristic distances between pairs of leaf nodes (pdist) and draw a phylogenetic tree object in a MATLAB figure window as a phylogram, cladogram, or radial treeplot (plot). Manipulate tree data by selecting branches and leaves using a specified criterion (select) and removing nodes (prune).
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