TreeNode.
tip_tip_distances
(endpoints=None)[source]¶Returns distance matrix between pairs of tips, and a tip order.
State: Experimental as of 0.4.0.
By default, all pairwise distances are calculated in the tree. If endpoints are specified, then only the distances between those tips are computed.
endpoints (list of TreeNode or str, or None) – A list of TreeNode objects or names of TreeNode objects
The distance matrix
ValueError – If any of the specified endpoints are not tips
See also
Notes
If a node does not have an associated length, 0.0 will be used and a
RepresentationWarning
will be raised.
Examples
>>> from skbio import TreeNode
>>> tree = TreeNode.read(["((a:1,b:2)c:3,(d:4,e:5)f:6)root;"])
>>> mat = tree.tip_tip_distances()
>>> print(mat)
4x4 distance matrix
IDs:
'a', 'b', 'd', 'e'
Data:
[[ 0. 3. 14. 15.]
[ 3. 0. 15. 16.]
[ 14. 15. 0. 9.]
[ 15. 16. 9. 0.]]