prodigal-gv 2.9.0 vs prodigal 2.6.3

[lonestarling]

apcamargo Hi, First of all, thank you for you excellent tools, i did some test on my virus metagenomic data by prodigal-gv and prodigal 2.6.3 in " p meta", and i finally get 2440739 proteins by prodiga-gv and 2496415 by prodigal 2.6.3, a little bit different in them. acctually, i don't know how to choose them.

And in the study " Metagenomic compendium of 189680 DNA virues from the human gut microbiome" by Stephen Nayfach, they have choosen the code (4) TGA and code(15) TAG and code (90) TAA besides the standard code (11), and then chooe the results accoding the potential score for every predicted gene. but't i haven't understand how to change the code in meta mode. and i don't how how much it changes the outcome in this way compare to the code 11 only.

So can you give me some advice.
Sincerely yours L