skbio.tree.bme#

skbio.tree.bme(dm, allow_edge_estimation=True)[source]#

Perform balanced minimum evolution (BME) for phylogenetic reconstruction.

Parameters:

dmskbio.DistanceMatrix: Input distance matrix containing distances between taxa.
allow_edge_estimationbool, optional: Whether to perform an OLS-based estimation of branch lengths (True, default) or return a tree without branch lengths assigned (False).

Returns:

TreeNode: Reconstructed phylogenetic Tree with estimated edge values (if allow_edge_estimation is True).

See also

gme
nj

Notes

Balanced Minimum Evolution (BME) is a refinement of the distance-based minimum evolution problem where average distances between subtrees ignores the size of the subtrees. The BME algorithm implemented here uses the same OLS based edge estimation used with Greedy Minimum Evolution (GME).

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 bme

>>> 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'])

Perform Balanced Minimum Evoltuion (BME) and construct the minimum evolution tree representing the relationship between those taxa. This is returned as a TreeNode object.

>>> tree = bme(dm)
>>> print(tree.ascii_art())
                    /-monkey
-human--- /--------|
                   |          /-pig
                    \--------|
                             |          /-chicken
                              \--------|
                                        \-rat

Notice that, unlike neighbor joining, the tree is rooted at a taxa/leaf node. This will allow it to have nearest neighbor interchange performed on it without needing to re-root the tree.