augur.refine module

Refine an initial tree using sequence metadata.

exception augur.refine.InvalidUseOfRemoveOutgroup(root)

Bases: AugurError

Raised when –remove-outgroup is used with an invalid –root option.

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.root_outside_of_treetime(T, root, is_timetree, remove_outgroup)

If the requested root(ing approach) is possible to do without TreeTime then this function modifies T in place, and returns None. If the rooting approach requires TreeTime then we return a string to be supplied to TreeTime as its root/reroot arguments.

augur.refine.run(args)