exp.py

import random
import dendropy
from dendropy import treesim

def generate(birth_rates, death_rates):
    assert len(birth_rates) == len(death_rates)
    tree = dendropy.Tree()
    for i, br in enumerate(birth_rates):
        tree = treesim.birth_death(birth_rates[i],
                                   death_rates[i],
                                   max_time=random.randint(1,8),
                                   tree=tree,
                                   assign_taxa=False,
                                   repeat_until_success=True)
        print(tree.as_string('newick'))
    tree.randomly_assign_taxa(create_required_taxa=True)
    return tree

tree = generate([0.1, 0.6, 0.1], [0.1, 0.6, 0.1])
print(tree.as_string('newick'))

import dendropy

citation = """\
@article{HeathHH2012,
	Author = {Tracy A. Heath and Mark T. Holder and John P. Huelsenbeck},
	Doi = {10.1093/molbev/msr255},
	Journal = {Molecular Biology and Evolution},
	Number = {3},
	Pages = {939-955},
	Title = {A {Dirichlet} Process Prior for Estimating Lineage-Specific Substitution Rates.},
	Url = {http://mbe.oxfordjournals.org/content/early/2011/11/04/molbev.msr255.abstract},
	Volume = {29},
	Year = {2012}
	}
"""


dataset = dendropy.DataSet.get_from_string(
        "(A,(B,(C,(D,E))));",
        "newick")
dataset.annotations.add_citation(citation)
print dataset.as_string("nexml")