upgma

biotite.sequence.phylo.upgma(distances)

Perform hierarchical clustering using the unweighted pair group method with arithmetic mean (UPGMA).

This algorithm produces leaf nodes with the same distance to the root node. In the context of evolution this means a constant evolution rate (molecular clock).

Parameters:

distancesndarray, shape=(n,n)

Pairwise distance matrix.

Returns:

treeTree

A rooted binary tree. The index attribute in the leaf TreeNode objects refer to the indices of distances.

Raises:

ValueError

If the distance matrix is not symmetric or if any matrix entry is below 0.

Examples

>>> distances = np.array([
...     [0, 1, 7, 7, 9],
...     [1, 0, 7, 6, 8],
...     [7, 7, 0, 2, 4],
...     [7, 6, 2, 0, 3],
...     [9, 8, 4, 3, 0],
... ])
>>> tree = upgma(distances)
>>> print(tree.to_newick(include_distance=False))
((4,(3,2)),(1,0));

Gallery

Dendrogram of a protein family

Dendrogram of a protein family

Dendrogram of a substitution matrix

Dendrogram of a substitution matrix