Smith-Waterman Score Settings

[samt]

Hi,

I am wondering if anyone has a good reference or tool to calculate parameters for Smith-Waterman mappers (e.g. Shrimp). I have found that most mappers readme are inadequate

I want to calculate edit distances and take into account gaps, mismatches and such but am not sure how this works and how to set the parameters such as M, H, and I

Thanks