how to set parameters for a specified sequence divergence value?

[wjj666]

Hello,

I want to alignment a query sequence with up to 30% sequence divergence or higher (may be up to 40% sequence divergence). Could you please tell me how to set the parameters for that?

Thank you very much.

[lh3]

Minimap2 won't work well for this large divergence. Probably last, blastz or other cross-species aligners will be better.