Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

I've downloaded he source code to see how this can be done but couldn't find it. There is some options in some of the files for different BLOSUM matrices but I don't think you can change it in the main function. Anyway, I don't expect it to have a large impact