I can recommend SNAP as an easy to use and train eukaryotic gene prediction software: http://www.ncbi.nlm.nih.gov/pubmed/15144565

If SNAP works for you, you can also try using MAKER, which wraps SNAP and other annotation tools into a pipeline that can be viewed and edited in Apollo.

Hi Gregor,

I am a member of the group that developed the geneid ab initio gene prediction software. I see your post is quite old but thought I would reply anyway. I am sorry you had trouble training geneid. I assume you followed the step-by-step training tutorial that can be found in http://genome.crg.es/software/geneid/training.html.

Nowadays we actually have a semi-automated gene training pipeline that simplifies the training process. It does require you be familiar with command line linux and we are currently in the process of making a package that could be downloaded and installed locally in a linux environment. We hope to have this available by the end of the summer. In the mean time anyone interested in having a geneid parameter file for their species may contact us.

Please note that geneid already has a large number of species-specific matrices. You may access them by going here:

http://genome.crg.es/software/geneid/index.html#parameters

Regards,
Francisco Camara (http://big.crg.cat/people/fcamara)
Center for Genomic Regulation (CRG)
Computational Biology of RNA Processing