Recombination mode (--recombi-mode) allows users to select two other sequences (--recombi-references SEQ_ID1,SEQ_ID2) from their MSA to colour SNPs by. SNPs in the snipit plot will be coloured by if they are present in recombination reference 1, recombination reference 2, both references, or private mutations.
Recombination mode (
--recombi-mode) allows users to select two other sequences (--recombi-references SEQ_ID1,SEQ_ID2) from their MSA to colour SNPs by. SNPs in the snipit plot will be coloured by if they are present in recombination reference 1, recombination reference 2, both references, or private mutations.