[maker-devel] Long introns from Augustus

[Shane Brubaker]

Hi, we have a very compact genome and we are getting a lot of fused gene models from running Augustus.  I am wondering if anyone has any advice about how to prevent introns above a certain cutoff from being created?

I tried a couple of things, some settings in a probabilities file and also changing a long list of probabilities to another file that someone had suggested on a forum.  So far I don't really see any changes though.

Any advice would be greatly appreciated.  

Thanks,
Shane