skbio.tree.TreeNode.root_at_midpoint

TreeNode.root_at_midpoint(reset=False, branch_attrs=['name'], root_name='root', inplace=False)

Reroot the tree at the midpoint of the two tips farthest apart.

Parameters:

resetbool, optional

Whether to remove the original root of a rooted tree before performing the rerooting operation. Default is False.

Added in version 0.6.2.

Note

The default value will be set as True in 0.7.0.

branch_attrsiterable of str, optional

Attributes of each node that should be considered as attributes of the branch connecting the node to its parent. This is important for the correct rerooting operation. “length” and “support” will be automatically included as they are always branch attributes.

Added in version 0.6.2.

Note

name will be removed from the default in 0.7.0, as it is usually considered as an attribute of the node instead of the branch.

root_namestr or None, optional

Name for the new root node, if it doesn’t have one.

Added in version 0.6.2.

Note

The default value will be set as None in 0.7.0.

inplacebool, optional

Whether to reroot the tree in place (True) or to create a rerooted copy of the tree (False, default).

Added in version 0.6.3.

Returns:

TreeNode

A tree rooted at its midpoint.

Raises:

TreeError

If a tip ends up being the mid point.

LengthError

Midpoint rooting requires length and will raise (indirectly) if evaluated nodes don’t have length.

Warning

The default behavior of root_at_midpoint is subject to change in 0.7.0. The new default behavior can be achieved by specifying reset=True, branch_attrs=[], root_name=None.

See also

root_at

unrooted_copy

Notes

The midpoint rooting (MPR) method was originally described in [1].

Tree caches (see details) will not be retained in the returned tree. In in-place mode, they will be cleared prior to rerooting. In copying mode, they will not be copied to the new tree.

References

[1]

Farris, J. S. (1972). Estimating phylogenetic trees from distance matrices. The American Naturalist, 106(951), 645-668.

Examples

>>> from skbio import TreeNode
>>> tree = TreeNode.read(["((a:1,b:1)c:2,(d:3,e:4)f:5,g:1)h;"])
>>> print(tree.ascii_art())
                    /-a
          /c-------|
         |          \-b
         |
-h-------|          /-d
         |-f-------|
         |          \-e
         |
          \-g

>>> t = tree.root_at_midpoint(branch_attrs=[])
>>> print(t)
((d:3.0,e:4.0)f:2.0,((a:1.0,b:1.0)c:2.0,g:1.0)h:3.0)root;

>>> print(t.ascii_art())
                    /-d
          /f-------|
         |          \-e
-root----|
         |                    /-a
         |          /c-------|
          \h-------|          \-b
                   |
                    \-g