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, stochastic_resolve=False, max_iter=2, precision='auto', infer_gtr=True, Tc=0.01, reroot=None, use_marginal='always', fixed_pi=None, use_fft=True, clock_rate=None, clock_std=None, clock_filter_iqd=None, verbosity=1, covariance=True, rng_seed=None, **kwarks)
- augur.refine.register_parser(parent_subparsers)
- augur.refine.run(args)