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.
Parameters: | endpoints (list of TreeNode or str, or None) – A list of TreeNode objects or names of TreeNode objects |
---|---|
Returns: | The distance matrix |
Return type: | DistanceMatrix |
Raises: | 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.]]