MOLBIO SOFT. SITES /LINUX SW

Harry Mangalam mangalam at uci.edu
Mon Mar 6 12:19:08 EST 1995


In article <3j75cf$8mi at owl.und.ac.za>, dace at shrike.und.ac.za (Roy Dace) wrote:

> Andrew Martin (martin at bsm.bioc.ucl.ac.uk) wrote:
> : Run the free Linux Unix clone on your new PC and you'll have access to the
> : whole world of free Unix software. Have a look at 
> : http://sunsite.unc.edu/mdw/linux.html for information on Linux.
> 
> Hi,
> 
> I'm also a Linux user but I'm wondering if you've seen any software of
> specific interest to molecular biologists available for the OS.  I'm
> specifically looking for a program to help select PCR primers and (for
> a different project) a port of one which can do cladistic anaylsis.
> of PCR RAPD's.

I've  "ported" Ladeanna Hillier/Phil Green's Oligo Selection Program OSP
(text and X windows version) to Linux (essentially a straight recompile,
commenting out some Linux-confusing X11 code).

Someone has ported the GDE package to Linux, altho it may be a rev out of
date; I believe the ACEdb package runs fine on Linux, essentially anything
that requires std libs and POSIX-like system calls should compile OK on
LInux (Higgins' clustal v/w, Prestridge's signalscan, Gilbert's READSEQ
and now Seqpup (I think..haven't tried it yet), etc.   Specifically
excluded are any programs that use special libs or expect special hardware
configurations (notably SGI's GL libs, and graphics hardware, although
this should change soon with the release of OpenGL (the 'Open' version of
SGI's GL, which allows previously SGI-only software runnable on Suns, HPs,
DEC Alphas, etc) and PC implementations of 3D video hardware using the
GLint chips and others.


I would imagine that Joe Felsenstein's Phylip pkg ports over pretty easily
as well, if he hasn't done it already ....ahhhh, it has been - it was at
least partly written on it:

from Joe hisself:

   Fourie Joubert asked if any molecular biology applications have been
   ported to Linux.  I suspect nearly everything that is distributed as
   Unix C source will work fine.  I use Linux on my laptop as one of the
   systems I develop my phylogeny package PHYLIP on, and the 3.5c version which
   is in C source code compiles and works with no problems.

   -----
   Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
   Internet:         joe at genetics.washington.edu     (IP No. 128.95.12.41)
 Bitnet/EARN:      felsenst at uwavm


Mail me for more info...
Cheers
harry
-- 
Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine,
      Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598
                 --- knowledge is fractal ---
            http://hornet.mmg.uci.edu/~hjm/hjm.html
  Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW 




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