Gene clustering in annotation pipeline

Question

[Mike]

Hello all,

I have data from various sources and would like to combine them the best way possible in order to eventually predict the genes in eukaryotics. The inputs include ab-initio predictions, transcriptome built from rna-seq and protein sequences alignments as well as data from similar species.

I'm having trouble doing that, I tried using EVidenceModeler (EVM) but with much difficulty. I hope you can help me regarding gene clustering and combining my data, any known methods to do so?

To further explain, here are samples from the data:

I'm not sure how much of it should I code myself or are there recommended tools for combining this type of data?

Any help is highly appreciated, thank you.