# biotite.sequence.phylo.upgma¶

biotite.sequence.phylo.upgma(distances)

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

Parameters: distances : ndarray, shape=(n,n) Pairwise distance matrix. tree : Tree A rooted binary tree. The index attribute in the leaf TreeNode objects refer to the indices of distances. 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));