I am planning to use Maker predicted genes for identifying orthologs among the closely related species. But Maker has predicted multiple transcripts for each locus (because of multiple gene predictors that were used in Maker as well as multiple isoforms for the genes). Although, I am using only predictions with AED scores <1.0, I still have many models for each locus. My question is, what is the best way to chose a transcript for a region? Should I select the longest coding sequence for that region? Are there any program that can perform this step?
Thanks for any help!