augur translate

Translate gene regions from nucleotides to amino acids.

usage: augur translate [-h] [--tree TREE]
                       [--ancestral-sequences ANCESTRAL_SEQUENCES]
                       --reference-sequence REFERENCE_SEQUENCE
                       [--genes GENES [GENES ...]]
                       [--output-node-data OUTPUT_NODE_DATA]
                       [--alignment-output ALIGNMENT_OUTPUT]
                       [--vcf-reference-output VCF_REFERENCE_OUTPUT]
                       [--vcf-reference VCF_REFERENCE]

Named Arguments


prebuilt Newick – no tree will be built if provided


JSON (fasta input) or VCF (VCF input) containing ancestral and tip sequences


GenBank or GFF file containing the annotation


genes to translate (list or file containing list)


name of JSON file to save aa-mutations to


write out translated gene alignments. If a VCF-input, a .vcf or .vcf.gz will be output here (depending on file ending). If fasta-input, specify the file name like so: ‘my_alignment_%GENE.fasta’, where ‘%GENE’ will be replaced by the name of the gene


fasta file where reference sequence translations for VCF input will be written


fasta file of the sequence the VCF was mapped to