augur reconstruct-sequences

Reconstruct alignments from mutations inferred on the tree

usage: augur reconstruct-sequences [-h] --tree TREE [--gene GENE] --mutations
                                   [--vcf-aa-reference VCF_AA_REFERENCE]
                                   [--internal-nodes] [--output OUTPUT]

Named Arguments


tree as Newick file


gene to translate (list or file containing list)


json file containing mutations mapped to each branch and the sequence of the root.


fasta file of the reference gene translations for VCF format


include sequences of internal nodes in output

Default: False