augur.ancestral
Infer ancestral sequences based on a tree.
The ancestral sequences are inferred using TreeTime. Each internal node gets assigned a nucleotide sequence that maximizes a likelihood on the tree given its descendants and its parent node. Each node then gets assigned a list of nucleotide mutations for any position that has a mismatch between its own sequence and its parent’s sequence. The node sequences and mutations are output to a node-data JSON file.
If amino acid options are provided, the ancestral amino acid sequences for each requested gene are inferred with the same method as the nucleotide sequences described above. The inferred amino acid mutations will be included in the output node-data JSON file, with the format equivalent to the output of augur translate.
The nucleotide and amino acid sequences are inferred separately in this command, which can potentially result in mismatches between the nucleotide and amino acid mutations. If you want amino acid mutations based on the inferred nucleotide sequences, please use augur translate.
Note
The mutation positions in the node-data JSON are one-based.
- augur.ancestral.ancestral_sequence_inference(tree=None, aln=None, ref=None, infer_gtr=True, marginal=False, fill_overhangs=True, infer_tips=False, alphabet='nuc')
infer ancestral sequences using TreeTime
- Parameters
tree (Bio.Phylo.BaseTree.Tree or str) – tree or filename of tree
aln (Bio.Align.MultipleSeqAlignment or str) – alignment or filename of alignment
ref (str, optional) – reference sequence to pass to TreeTime’s TreeAnc class
infer_gtr (bool, optional) – Description
marginal (bool, optional) – Description
fill_overhangs (bool) – In some cases, the missing data on both ends of the alignment is filled with the gap character (‘-‘). If set to True, these end-gaps are converted to “ambiguous” characters (‘N’ for nucleotides, ‘X’ for aminoacids). Otherwise, the alignment is treated as-is
infer_tips (bool) – 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
alphabet (str) – alphabet to use for ancestral sequence inference. Default is the nucleotide alphabet that included a gap character ‘nuc’. Alternative is aa for amino acids.
- Returns
treetime.TreeAnc instance
- Return type
- augur.ancestral.collect_mutations_and_sequences(tt, infer_tips=False, full_sequences=False, character_map=None, is_vcf=False)
iterates of the tree and produces dictionaries with mutations and sequences for each node.
- Parameters
tt (treetime.TreeTime) – instance of treetime with valid ancestral reconstruction
infer_tips (bool, optional) – if true, request the reconstructed tip sequences from treetime, otherwise retain input ambiguities
full_sequences (bool, optional) – if true, add the full sequences
character_map (None, optional) – optional dictionary to map characters to a custom set.
- Returns
dictionary of mutations and sequences
- Return type
- augur.ancestral.register_parser(parent_subparsers)
- augur.ancestral.run(args)
- augur.ancestral.run_ancestral(T, aln, root_sequence=None, is_vcf=False, full_sequences=False, fill_overhangs=False, infer_ambiguous=False, marginal=False, alphabet='nuc')