Neighbor-joining

Inference: Neighbor-Joining¶

Neighbor-joining infers a tree from a distance matrix without assuming a molecular clock.

In [ ]:

import toytree

tree = toytree.rtree.unittree(8, seed=321)
dist = tree.distance.get_tip_distance_matrix()
nj = toytree.infer.neighbor_joining_tree(dist)
# optional: root the unrooted tree for display
nj = nj.mod.root_on_minimal_ancestor_deviation()
c, a, m = nj.draw(layout='r', tip_labels=True, scale_bar=True)
c

import toytree tree = toytree.rtree.unittree(8, seed=321) dist = tree.distance.get_tip_distance_matrix() nj = toytree.infer.neighbor_joining_tree(dist) # optional: root the unrooted tree for display nj = nj.mod.root_on_minimal_ancestor_deviation() c, a, m = nj.draw(layout='r', tip_labels=True, scale_bar=True) c