augur.refine module¶
Refine an initial tree using sequence metadata.
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augur.refine.
collect_node_data
(T, attributes)¶
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augur.refine.
refine
(tree=None, aln=None, ref=None, dates=None, branch_length_inference='auto', confidence=False, resolve_polytomies=True, max_iter=2, 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)¶
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augur.refine.
register_arguments
(parser)¶
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augur.refine.
run
(args)¶