Re: [Fink-beginners] updating fink to OS 10.8.3

[Alexander H. <ale...@gm...>]

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/