Calculating tree diameter

Question

[Joe]

Hi all,

I'm hoping someone has a 'ready-to-go' one liner or tool suggestion for finding the 2 most distant tips of a binary/phylogenetic tree (a.k.a. its 'diameter')?

The algorithm itself seems straightforward, but I'm almost certain someone would have needed to do this before me.

Answer 1

[Joe]

Got it :)

Install dendropy and get the max distances in a distance matrix.

import dendropy

tree = dendropy.Tree.get(path='mytree',schema='format')
pdm = tree.phylogenetic_distance_matrix()
m1, m2 = pdm.max_pairwise_distance_taxa()
m1
<Taxon 0x7f8350358c10 'Taxon 1'>
m2
<Taxon 0x7f8350358f90 'Taxon 2'>