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skbio.tree.nni#

+
+
+skbio.tree.nni(tree, dm, inplace=True)[source]#
+

Perform nearest neighbor interchange (NNI) on a phylogenetic tree.

+
+
Parameters:
+
+
treeskbio.TreeNode

Input phylogenetic tree to be rearranged.

+
+
dmskbio.DistanceMatrix

Input distance matrix containing distances between taxa.

+
+
inplacebool, optional

Whether manipulate the tree in place (True, default) or return a +copy of the tree (False).

+
+
+
+
Returns:
+
+
TreeNode

Rearranged phylogenetic tree (if inplace is True).

+
+
+
+
+

Notes

+

NNI algorithm for minimum evolution problem on phylogenetic trees. It rearranges +an initial tree topology by performing subtree exchanges such that the distance +is minimized. This implementation is based on the FastNNI algorithm [1].

+

The input tree is required to be binary and rooted at a leaf node such that +there is a unique descendant from the root.

+

References

+
+
+[1] +

Desper R, Gascuel O. Fast and accurate phylogeny reconstruction +algorithms based on the minimum-evolution principle. J Comput Biol. +2002;9(5):687-705. doi: 10.1089/106652702761034136. PMID: 12487758.

+
+
+

Examples

+

Define a new distance matrix object describing the distances between five +taxa: human, monkey, pig, rat, and chicken.

+
>>> from skbio import DistanceMatrix
+>>> from skbio.tree import nj
+
+
+
>>> dm = DistanceMatrix([[0, 0.02,  0.18,  0.34,  0.55],
+...                      [0.02,  0, 0.19, 0.35,  0.55],
+...                      [0.18, 0.19,  0,  0.34,  0.54],
+...                      [0.34, 0.35,  0.34,  0,  0.62],
+...                      [0.55,  0.55,  0.54,  0.62,  0]],
+...                      ['human','monkey','pig','rat','chicken'])
+
+
+

Also, provide a tree topology to be rearranged. The tree provided is +required to be a binary tree rooted at a leaf node.

+

Note that the tree provided does not require to have assigned edge lengths.

+
>>> from skbio.tree import TreeNode
+
+
+
>>> tree = TreeNode.read(["(((human,chicken),(rat,monkey)))pig;"])
+>>> print(tree.ascii_art())
+                              /-human
+                    /--------|
+                   |          \-chicken
+-pig----- /--------|
+                   |          /-rat
+                    \--------|
+                              \-monkey
+
+
+

Perform nearest neighbor interchange (NNI). By default, the tree is +rearrangede in place.

+
>>> nni(tree, dm)
+>>> print(tree.ascii_art())
+                              /-rat
+                    /--------|
+                   |          \-chicken
+-pig----- /--------|
+                   |          /-monkey
+                    \--------|
+                              \-human
+
+
+

Besides rearranging the tree, estimated edge lengths are assigned to the +tree.

+
>>> rat = tree.find('rat')
+>>> print(rat.length)
+0.21
+
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