skbio.tree.TreeNode.root_at_midpoint#

TreeNode.root_at_midpoint()[source]#

Return a new tree rooted at midpoint of the two tips farthest apart.

This method doesn’t preserve the internal node naming or structure, but does keep tip to tip distances correct. Uses unrooted_copy but operates on a full copy of the tree.

Returns:

TreeNode: A tree rooted at its midpoint
LengthError: Midpoint rooting requires length and will raise (indirectly) if evaluated nodes don’t have length.

Raises:

TreeError: If a tip ends up being the mid point

See also

root_at
unrooted_deepcopy

Examples

>>> from skbio import TreeNode
>>> tree = TreeNode.read(["(((d:1,e:1,(g:1)f:1)c:1)b:1,h:1)a:1;"])
>>> print(tree.root_at_midpoint())
((d:1.0,e:1.0,(g:1.0)f:1.0)c:0.5,((h:1.0)b:1.0):0.5)root;