augur.ancestralο
Infer ancestral sequences based on a tree.
- augur.ancestral.ancestral_sequence_inference(tree=None, aln=None, ref=None, infer_gtr=True, marginal=False, fill_overhangs=True, infer_tips=False)ο
infer ancestral sequences using TreeTime
- Parameters
tree (Bio.Phylo tree or str) β tree or filename of tree
aln (Bio.Align.MultipleSeqAlignment or str) β alignment or filename of alignment
infer_gtr (bool, optional) β Description
marginal (bool, optional) β Description
fill_overhangs (bool) β In some cases, the missing data on both ends of the alignment is filled with the gap character (β-β). If set to True, these end-gaps are converted to βambiguousβ characters (βNβ for nucleotides, βXβ for aminoacids). Otherwise, the alignment is treated as-is
infer_tips (bool) β Since v0.7, TreeTime does not reconstruct tip states by default. This is only relevant when tip-state are not exactly specified, e.g. via characters that signify ambiguous states. To replace those with the most-likely state, set infer_tips=True
- Returns
treetime.TreeAnc instance
- Return type
TreeAnc
- augur.ancestral.collect_mutations_and_sequences(tt, infer_tips=False, full_sequences=False, character_map=None, mask_ambiguous=True)ο
iterates of the tree and produces dictionaries with mutations and sequences for each node.
- Parameters
tt (treetime) β instance of treetime with valid ancestral reconstruction
infer_tips (bool, optional) β if true, request the reconstructed tip sequences from treetime, otherwise retain input ambiguities
full_sequences (bool, optional) β if true, add the full sequences
character_map (None, optional) β optional dictionary to map characters to a custom set.
- Returns
dictionary of mutations and sequences
- Return type
dict
- augur.ancestral.register_parser(parent_subparsers)ο
- augur.ancestral.run(args)ο