On 5/25/13 10:07 AM, Robert Wohlhueter wrote: > Alex, > > Before I give you my "priority list", let me tell you that I am a > retired biochemist/molecular biologist, enjoying my retirement years as > an adjunct professor in Chemistry at Georgia State University -- a sort > of hobby scientist, trying to remediate a bioinformatics approach I was > too old to participate in from scratch. > > That said, I'll keep my list of packages I would like to see updated to > 10.8.x to the "sci" category. > > 1) "clustawl" and/or "tcoffee" are very widely used and indispensible > sequence alignment programs. Hard to judge which is best; clustawl is > more widely used. > > 2) The "ncbitools", particularly the "blash" modules are workhorses of > molecular biology database searching. There may be alternative > approaches to getting NCBI service on Mac 10.8 -- I'm looking at the > possibiities. > > 3) In my active, working years, "emboss" (we ran in on unix boxes) was > our every0day, comprehensive sequence analyis package. I personally > don't use it these days -- but it remains prominant. > > 4) "hmmer" is a mature and widely used, hidden Markov approach > characterizing protein (that's how I use it) sequence characteristics, > with which one can then search the databases for proteins with similar > characteristics. > > 5) "phylip" is perhaps a little out-moded in the field, but the only > representive of phylogenetic inference software in the fink package > collection. > > 6) I personally am a fan of the "snna" neural net software. It is > flexible and comprehensive; perhaps not much updating since it's > introduction in the '90's, but (I find) more accessible than, say, the > NN modules of Octave (or MATLAB) > > Even if some or all of them were ported as "unstable", I'd be happy to > give them a spin and report my experiences. > > Bob Wohlhueter > >
Nah, we deliberately got rid of unstable because people didn't migrate stuff back out. :-) Clustalw is already available, in the guise of the "clustalw2" package, and I just migrated phylip. We can look at migrating the others. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may _______________________________________________ Fink-beginners mailing list Fink-beginners@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.beginners Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-beginners
