It depends on how diverse the genus is, and will likely need to adjust the k-mer length range away from the defaults as longer k-mers are likely to mismatch with a lot of diversity. I would run in mode --create-db with the option --plot-fit 10 first to make sure you are getting reasonable straight line fits for your k-mer range, and adjust with --min-k and --max-k if not.
After that, the first level clusters should be the species divides. You may need to attempt the fit iteratively to get these at the desired level of specificity.
It depends on how diverse the genus is, and will likely need to adjust the k-mer length range away from the defaults as longer k-mers are likely to mismatch with a lot of diversity. I would run in mode
--create-dbwith the option--plot-fit 10first to make sure you are getting reasonable straight line fits for your k-mer range, and adjust with--min-kand--max-kif not.After that, the first level clusters should be the species divides. You may need to attempt the fit iteratively to get these at the desired level of specificity.