augur.ancestral module¶
Infer ancestral sequences based on a tree.
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augur.ancestral.
ancestral_sequence_inference
(tree=None, aln=None, ref=None, infer_gtr=True, marginal=False, fill_overhangs=True)¶ infer ancestral sequences using TreeTime
- Parameters
tree (Bio.Phylo tree or str) – tree or filename of tree
aln (Bio.Align.MultipleSeqAlignment or str) – alignment or filename of alignment
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
- Returns
treetime.TreeAnc instance
- Return type
TreeAnc
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augur.ancestral.
collect_sequences_and_mutations
(T, is_vcf=False)¶ iterates of the tree and produces dictionaries with mutations and sequences for each node.
- Parameters
T (Bio.Phylo.Tree) – Phylogenetic tree decorated with sequences and mutations as output by treetime.
is_vcf (bool, optional) – specifies whether input alignment was vcf type (implying long genomes)
- Returns
dictionary of mutations and sequences
- Return type
dict
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augur.ancestral.
register_arguments
(parser)¶
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augur.ancestral.
run
(args)¶