bio-phylo-tree-manipulation

Root with Outgroup

tree = Phylo.read('tree.nwk', 'newick')

## Root with multiple taxa (must be monophyletic)

outgroup = [{'name': 'TaxonA'}, {'name': 'TaxonB'}]
if tree.is_monophyletic(outgroup):
    tree.root_with_outgroup(*outgroup)
else:
    print('Outgroup is not monophyletic')

Check if tree is rooted (bifurcating at root)

print(f'Is bifurcating: {tree.is_bifurcating()}')