biotite.sequence.phylo.upgma¶
- biotite.sequence.phylo.upgma(distances)[source]¶
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 the BLOSUM62 matrix
Dendrogram of the BLOSUM62 matrix
Similarity of HCN and related channels
Similarity of HCN and related channels