Generate distance matrix from newick tree

dist_matrix.py

from itertools import product
import pandas as pd
from ete3 import Tree

t = Tree("some_tree_file.nwk")

leaves = t.get_leaves()
leaf_names = t.get_leaf_names()
pair = product(leaves, leaves)

dist = {(each[0].name, each[1].name): each[0].get_distance(each[1]) for each in pair}
df = pd.DataFrame(index=leaf_names, columns=leaf_names).fillna(0).stack().reset_index()
df["dist"] = df.apply(lambda x: dist[(x["level_0"], x["level_1"])], axis=1)