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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."
There have been a lot of Ask Slashdot's about software for molecular munging, genetic gerrymandering and physical futzing. All your questions can be answered in one location.
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Linux MAPI Server!
http://www.openone.com/software/MailOne/
(Exchange Migration HOWTO coming soon)
http://www.sanger.ac.uk/Software/EMBOSS/
it's a set of command line tools in developpement, under the GPL.
And maybe other things in http://www.sanger.ac.uk/Software/ may interest you
It is truly pitiful that a grad student is asking slashdot for advice. You would be much better off walking down the hall or waiting for a department meeting and ask people what they use. Read papers and see what packages they use. I'll give you advice anyway, because I feel sorry for you. A place to start would be Biocat.
Scuttlemonkey is a troll
Your question is too general. You do not need to install anything if your needs are limited to aligment of few DNA/protein fragments once a week. The web resources will be good enough for that. For any lab doing sequencing I highly recommend Staden The gap4 program, which is a part of a package is a category leader. You may also take a look at Sanger Centre web site: Software. Almost all what you may ever need is there. ;-)