I'm planning to do a de novo plant genome annotation of using Maker-p software. I've completed the installation steps as per the reference (http://gmod.org/wiki/MAKER_Tutorial_2013). Also did a trial run and everything seems to be good. My question is that,
1) Is it mandatory to train the augustus or snap for de novo gene prediction?
2) I've seen some articles related with this incorporated repeatrunner in addition to repeatmasker. but, i didn't install it with Maker-p. Is it affect the maker annotation quality?
Please give me a clarification regarding this....Thank you