See https://github.com/jeetsukumaran/DendroPy/issues/53

labels-as-support.py

#! /usr/bin/env python

import dendropy

def get_tree(r):
    tree_str = "((C:1.3,D:4.)34:0.034,(A:1.1,(B:1.2,X:1.6)26:0.026)12:0.0126,E:1.5);"
    tree = dendropy.Tree.get(
            data=tree_str,
            schema="newick",
            rooting=r,
            )
    return tree

def node_label_method():
    tree = get_tree("force-rooted")
    outgroup_node = tree.find_node_with_taxon_label("X")
    new_root = outgroup_node.parent_node
    tree.reseed_at(new_root)
    return tree

def rooted_bipartition_method(r):
    tree = get_tree(r)
    benc = tree.encode_bipartitions()
    support_values = {}
    for nd in tree:
        support_values[nd.bipartition] = float(nd.label) if nd.label is not None else 1.0

    outgroup_node = tree.find_node_with_taxon_label("X")
    new_root = outgroup_node.parent_node
    tree.reseed_at(new_root)
    tree.encode_bipartitions()
    for nd in tree:
        nd.label = support_values.get(nd.bipartition, "Not_specified_in_original_tree")
    tree.seed_node.edge.length = None

    return tree

print("\n[Original Tree:]\n    ")
print(get_tree("force-rooted").as_string("newick").strip())
print("\n[Labels-attached-to-nodes Tree:]\n    ")
print(node_label_method().as_string("newick").strip())
print("\n[Labels-attached-to-unrooted-bipartition-method Tree:]\n    ")
print(rooted_bipartition_method("force-unrooted").as_string("newick").strip())
print("\n[labels-attached-to-rooted-bipartition-method Tree:]\n")
print(rooted_bipartition_method("force-rooted").as_string("newick").strip())