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.
Returns:  tree : Tree
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));