I use trinity, and want to use hmmer pfam.
But my trinity file is Nucleotide FASTA.
How can I codon it to Protein FASTA?
Another option would be to just run getORF with minimum ORF length on it. You will get more sequences but I -personally- wouldn't use transdecoder, it makes some very funny assumptions in its filtering heuristics, and I have read about very mixed results on Biostars.
Another option would be to run pfam from interproscan which can be run directly on nucleotide data.