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import sys
from dendropy import *
from dendropy.interop import paup
f=open('angio35.nex','r')
d=DataSet()
d.read(f,"nexus")
for x in d.char_matrices:
tree=paup.estimate_tree(x,tree_est_criterion='likelihood',num_states=2,unequal_base_freqs=True,gamma_rates=False,prop_invar=False)
print tree.as_string("newick")`!
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