Also, another question. Anything better than Transdecoder for the future, for euk protein calling? Last push on their repo is 4 years ago and no releases (if I found the correct one). I also don't see any .faa file, like in prodigal/pyrodigal

There is an

faa

it just has a different name --

.pep

? We're open to alternatives, but since we don't work a lot with eukaryotes in our research I'm not so familiar with what tools are out there.

Oh I see! Me neither, that's why I'm asking xD

Thanks. Both are a bit of an overkill since we have mature mRNAs and don't need to think about splicing. Transdecoder is from the Trinity project that focuses on transcriptomes so it only deals with mature mRNAs.