Re: Repeatmasker with RMBlastYou don’t need to do anything within MAKER. RMBlast is all configured within RepeatMasker. You just need to follow the documentation with RepeatMasker to set it up. MAKER will just run RepeatMasker however it is configured, so it doesn’t need to know if you’re using wublast, cross_match, or RMBlast. It’s all the same to MAKER.
If you’re wanting to use RMBlast as the BLAST engine for other programs outside of RepeatMasker (i.e. rather than running classic BLAST next time you’re performing a BLAST analysis, you run decide to run RMBlast), well you don’t really want to do that . In fact RMBlast warns not to do that on their website because the changes they made to the BLAST code may affect results for analyses outside of RepeatMasker. So you will need to install regular BLAST as well as RMBlast. Then RMBlast will be used by RepeatMasker and regular BLAST for everything else.