Extend the leaf branch lengths of a Newick tree so all the paths are the same length

newick_stretch.py

from Bio import Phylo
from io import StringIO
import sys

treedata = sys.argv[1]
handle = StringIO(treedata)
tree = Phylo.read(handle, "newick")

out = StringIO()

def path_length(tree, node):
    return sum(y.branch_length if y.branch_length else 0 for y in tree.get_path(node))

max_length = max([path_length(tree, x) for x in tree.get_terminals()])

for leaf in tree.get_terminals():
    q = path_length(tree, leaf)
    leaf.branch_length += max_length - q

Phylo.write([tree], out, "newick")
print(out.getvalue())