Example: Building a Phylogenetic Tree :: Phylogenetic Analysis (Bioinformatics Toolbox)

Bioinformatics Toolbox

Example: Building a Phylogenetic Tree

In this example, a phylogenetic tree is constructed from mitochondrial DNA (mtDNA) sequences for the family Hominidae. This family includes gorillas, chimpanzees, orangutans, and humans.

The following procedures demonstrate the phylogenetic analysis features in the Bioinformatics Toolbox. They are not intended to teach the process of phylogenetic analysis, but to show you how to use MathWorks products to create a phylogenetic tree from a set of nonaligned nucleotide sequences.

Overview for the Primate Example — Describes the biological background for this example.
Creating a Phylogenetic Tree for Five Species — Use the Jukes-Cantor method to calculate distances between sequences, and the Unweighted Pair Group Method Average (UPGMA) method for linking the tree nodes.
Creating a Phylogenetic Tree for Twelve Species — Add additional organisms to confirm the observed monophyletic groups.
Exploring the Phylogenetic Tree — Use the MATLAB command-line interface to programmatically determine characteristics in a phylogenetic tree.

For information on how to create a phylogenetic tree with multiply aligned sequences, see the function —phytree.

Phylogenetic Analysis

Overview for the Primate Example