Error: Gap penalty settings are not supported for this scoring matrix.

[cmayer]

I am doing a blastx search using default parameters except --gapopen N, since I think the default parameter should be lowered for my application. This gives me the error message: Error: Gap penalty settings are not supported for this scoring matrix.

In the documentation I did not find any indication why this is not allowed. For which scoring matrices would the gapopen parameter be allowed?

Many thanks!

[cmayer]

Well, the gapopen parameters was outside of the allowed range. But the error message is not correct. It gives the impression that the parameter cannot be used. If the error message would have told me that the parameter is outside the allowed range, this would have been more informative.

Thanks for this great program anyway!!!