They aren't many (most of it is closed source). The one package that is used a stupid amount is the Biopython package. Most synthetic biologists I know are pret

They aren't many (most of it is closed source). The one package that is used a stupid amount is the Biopython package. Most synthetic biologists I know are pretty much only trained in python (because bioinformatics), so use that package religiously. As examples of closed source software that there aren't good open source alternatives to, see Benchling and SnapGene. No good plasmid editors are open source and hackable.