augur.refine module

Refine an initial tree using sequence metadata.

augur.refine.collect_node_data(T, attributes)
augur.refine.refine(tree=None, aln=None, ref=None, dates=None, branch_length_inference='auto', confidence=False, resolve_polytomies=True, max_iter=2, precision='auto', infer_gtr=True, Tc=0.01, reroot=None, use_marginal=False, fixed_pi=None, clock_rate=None, clock_std=None, clock_filter_iqd=None, verbosity=1, covariance=True, **kwarks)
augur.refine.register_arguments(parser)
augur.refine.run(args)