augur ancestral
Infer ancestral sequences based on a tree.
usage: augur ancestral [-h] --tree TREE [--alignment ALIGNMENT]
[--output-node-data OUTPUT_NODE_DATA]
[--output-sequences OUTPUT_SEQUENCES]
[--inference {joint,marginal}]
[--vcf-reference VCF_REFERENCE]
[--output-vcf OUTPUT_VCF]
[--keep-ambiguous | --infer-ambiguous]
[--keep-overhangs]
Named Arguments
- --tree, -t
prebuilt Newick
- --alignment, -a
alignment in fasta or VCF format
- --output-node-data
name of JSON file to save mutations and ancestral sequences to
- --output-sequences
name of FASTA file to save ancestral sequences to (FASTA alignments only)
- --inference
Possible choices: joint, marginal
calculate joint or marginal maximum likelihood ancestral sequence states
Default: “joint”
- --vcf-reference
fasta file of the sequence the VCF was mapped to
- --output-vcf
name of output VCF file which will include ancestral seqs
- --keep-ambiguous
do not infer nucleotides at ambiguous (N) sites on tip sequences (leave as N).
Default: False
- --infer-ambiguous
infer nucleotides at ambiguous (N,W,R,..) sites on tip sequences and replace with most likely state.
Default: True
- --keep-overhangs
do not infer nucleotides for gaps (-) on either side of the alignment
Default: False