Best Mac OS X molecular biology software?

May 24, 2005 8:26 AM

MolecularBio geeks: What's the best sequence analysis software for OS X?

I need to do quite straightforward stuff: Fetch sequences from GenBank (and eventually from my lab's sequencer), run alignments and phylogenies. Nothing too fancy. I am playing around with MacGDE -- any other suggestions? Thanks!

posted by docgonzo to science & nature (7 comments total)

DNAStar is OK -- maybe newer versions are better. It's pretty simple to use, if not overly powerful. Maybe there's a free demo you could try out.
posted by sennoma at 9:37 AM on May 24, 2005

Do you need a GUI? All of the commercial apps can be supplanted with open-source or free command-line equivalents, or you can run stuff on the web.

MacVector is excellent and runs under OS X natively.

VectorNTI is comprehensive but does not run under Tiger. The developer has no plans to update this product to run under Tiger.
posted by AlexReynolds at 10:04 AM on May 24, 2005

Have you explored the tools available online? The NCBI website has a whole bunch of stuff and it's pretty easy to navigate. They have BLAST, of course. There are other sites for more esoteric stuff, but they are not quite as easy to use as NCBI. There's SRS which has a lot of tools, and the ClustalW tool for multiple alignments. You could also browse around the Expasy PROSITE and Pfam sites for other potentially useful tools and links (these 2 are for proteins, but you can translate DNA sequences into protein sequences using some of the BLAST tools at NCBI). Most sites will let you upload your own sequence in Fasta format, even though they are geared toward analyzing stuff that's already in various databases. There's some amazingly powerful tools available for free on the web, so you might not need to buy anything. Oh, and these work in Safari - that's what I use. I don't know about other browsers.
posted by Quietgal at 10:12 AM on May 24, 2005

I have usually been disappointed by alignments and phylogenies generated by commercial off-the-shelf software. They try to simplify stuff a little too much, in my experience. Fetching and displaying sequences should be pretty straightforward.

I would recommend trying the free and well-respected EMBOSS and its varoius front-ends, some of which are just for Mac OS X.
posted by grouse at 10:17 AM on May 24, 2005

Get Virtual PC and run BioEdit. I'm not kidding.
posted by gsb at 11:34 AM on May 24, 2005

Side note from a non-bio type -- phylogeny generators; how accurate and automated can they get? Are there any good free ones I can try?
posted by effugas at 2:47 PM on May 24, 2005

Phylogeny of what?

Accuracy: How do you want to determine how accurate the phylogeny is?

Automated: The more default parameters you use, the poorer your results will be.

PAML and Phylip are widely used. I have been told that little effort has gone into making PAML easy to use because doing so will only encourage people who don't know what they're doing to report spurious results.

Abandon all hope ye who enter here.
posted by grouse at 3:15 PM on May 24, 2005