Unix Software for Molecular Biology?

mircea asks: "I'm a graduate student, doing my thesis in molecular biology. I was wondering if there is any software available for Unix in the field. The functionality I'm looking for is somewhere between Generunner for Windows, by Hastings Software (now defunct, I think) and Lasergene, by Dnastar. At a minimum, it should do ORF analysis, primer design and secondary structure prediction. Pairwise and/or multiple alignments an added bonus, although there are standalone programs that do just this. GPL'ed preferred, of course :), but commercial solutions are OK, too. The existence of such software would make it much easier for me to sell my boss the idea of converting to Linux. Thanks for any ideas."