augur reconstruct-sequences

Reconstruct alignments from mutations inferred on the tree

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

Named Arguments

--tree

tree as Newick file

--gene

gene to translate (list or file containing list)

--mutations

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

--vcf-aa-reference

fasta file of the reference gene translations for VCF format

--internal-nodes

include sequences of internal nodes in output

Default: False

--output