I've enjoyed using hyphy quite a bit so far. Mostly I've been writing batch files. One problem I've encountered is that its very easy to introduce an error without knowing it. For example in setting constraints, a type-o can end up introducing a new variable.

Clearly better habits on the part of people writing batch files would help. (like always checking the number of parameters). But perhaps you guys could also come up with ways to help users avoid mistakes. Some sort of a preprocessor perhaps?

Anyway, thanks again for providing a useful tool.

Eliot

Dear Eliot,

I have been meaning to do something like that for a while. One of these days, the NIH or the NSF will actually fund HyPhy development directly (more or less), so we could hire a few people to help us maintain and develope the package better. As it is, I have no time to implement the features I'd like to put in, alas!

That said, there are some tricks to checking the batch code for validity. I'll try write them up and post the list here.

Cheers,
Sergei