Make a UPGMA cluster

Section author: Catherine Lozupone

An example of how to calculate the pairwise distances for a set of sequences.

Note

UPGMA should not be used for phylogenetic reconstruction.

Import a substitution model (or create your own)

Load the alignment.

Create a pairwise distances object calculator for the alignment, providing a substitution model instance.

Now use this matrix to build a UPGMA cluster.

We demonstrate saving this UPGMA cluster to a file.