Linux mol-bio/biochem software - a list. please mail additions

zinc zinc at zifi.genetics.utah.edu
Mon Oct 7 00:43:23 EST 1996


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here's the current list.  i spent most of today at the console
screwing with damned FORTRAN compilations - not something i enjoy.
anyway, thanks to the following people for their additions:

francis at ncbi.nlm.nih.gov (B.F. Francis Ouellette)
Ashok Aiyar <aiyar at ebv.oncology.wisc.edu>
gilbertd at chipmunk.bio.indiana.edu (Don Gilbert)

i will be converting the file to html some point this week.  since i
am having a difficult type focussing at this time, it will have to
wait.  if anyone tests this code and finds my observations to be
mistaken, please mail me (i'm sure you will :) ).

also, the text file is available from my web page, just not in html.
see http://zifi.genetics.utah.edu/~zinc/linux/linux.html for a link.

- -patrick finerty
biochem grad student, u of utah

==========================================================================


this site seems to have a lot of stuff:
ftp://nic.funet.fi:/pub/sci/molbio/emblmirror/unix/ 

this web pages lists quite bit of software as well:
http://mbisg2.sbc.man.ac.uk/gradschool/bioinf/prot.html


a lot of these are in FORTRAN so how well they compile is probably due
to how good the fortran support on a system is...

if i mention that i compiled or tested any of this stuff you might
want to know my system config.  generally, i keep zifi very
up-to-date, using linux/Documentation/Changes as a guide.  

here is my current config:

		Linux 2.1.1
		libc 5.4.7
		gcc 2.7.2
		g77-0.5.18.bin.tgz installed
		f2c-960717.elf.tgz
=======
something called VMD (Visual Molecular Dynamics) is almost ported: 
http://www.ks.uiuc.edu/Research/vmd/ 

=======

Molden	- Molden is a package for displaying Molecular Density from the
	  Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and
	  the Semi-Empirical packages Mopac/Ampac
	- main program is in fortran X-win driver in C
	- ftp://ftp.caos.kun.nl/pub/molgraph/molden

info at http://www.caos.kun.nl/~schaft/molden/molden.html

this compiled and ran on my system using the g77-0.5.18.bin.tgz
package from sunsite.  it took a ton of memory to compile - about 25
MB at one point so you should have some serious swap space or if asked
i'll make a binary available (my libc is prob too recent for most
people).  if you install the g77-0.5.18.bin.tgz package be sure to
link g77 to f77 because that's what make tries to use.  pretty cool. 

=======
RasMol	- displays pdb files, writes a variety of output formats.
	- current version is 2.6beta, written in C
	- ftp://ftp.dcs.ed.ac.uk/pub/rasmol
	- ftp://sunsite.unc.edu/pub/Linux/apps/biology/

i have used the beta version extensively under Linux.  it works like a
charm.  i did not encounter any bugs.  to compile for a 16 bpp
display, you must hack the Makefile produced with xmkmf.  change this
line: DEPTHDEF = -DEIGHTBIT to DEPTHDEF = -DSIXTEENBIT.  i did not
have luck just changing the value in rasmol.h as per the INSTALL
instructions. 

=======
MOLMOL	- MOLMOL is a molecular graphics program for displaying,
	  analyzing, and manipulating the three-dimensional structure
	  of biological macromolecules, with special emphasis on the
	  study of protein or DNA structures determined by NMR
	- version 2.2.0
	- ftp://ftp.mol.biol.ethz.ch/pub/software/MOLMOL
	- ftp://sunsite.unc.edu/pub/Linux/apps/biology/

requires motif to compile and ksh shell to run the script.  a binary
is available on sunsite (or mirrors). the binary works just fine on my
system.  if you use the binary, you also need to get the
molmol-2.2.0-doc.tgz file as well. be sure to move the binary to the
same place the doc files were unpacked.  run the install script and
then run the molmol script.

=======
XtalView- XtalView is a complete package for solving a macromolecular
	  crystal structure by isomorphous replacement, including
	  building the molecular model.
	- version ?, in fortran (crystallographers love fortran).  
	  have to sign a license to get source but not for binaries 

	- http://www.sdsc.edu/CCMS/Packages/XTALVIEW/

it looks like binaries are avail for Linux...(according to the above
page) but i didn't try to get any.

=======
WhatIf	- WHAT IF is a versatile protein structure analysis program
	  that can be used for mutant prediction, structure
	  verification, molecular graphics, etc. 
	- version ?, in FORTRAN
	- http://swift.embl-heidelberg.de/whatif/

licensed for a small fee to academics...

=======
Procheck- Checks the stereochemical quality of a protein structure,
	  producing a number of PostScript plots analysing its overall
	  and residue-by-residue geometry.  
	- version 3.4.3, written in FORTRAN
http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

obtain source from:
ftp://128.40.46.11/pub/procheck/tar3_4/procheck.tar.Z 

this is more fortran fun and games.  this would not compile with g77
as i ran out of memory at about 70 MB...

however, using the f2c package it compiled.  it seems to work ok.

another note, it took a really, really, really, really, long damned
time for 'clean' to compile.  i just went home...

=======
MOPAC	- you have to order this or something.  i couldn't find source
	  or much info.  any WWW search will bring up a ridiculous
	  number of online html manuals though.
	- ftp://129.79.74.206/

=======
i heard the GAMESS programs compile under Linux but i did not try them
as you have to go through a little effort to get them...

US version
GAMESS	- The General Atomic and Molecular Electronic Structure
	  System is a general ab initio quantum chemistry package.
	- version ?, written in ?
	- http://www.msg.ameslab.gov/GAMESS

site license is free to everyone but must sign a form... 

UK version
GAMESS	- GAMESS--UK is a general purpose ab initio molecular
	  electronic structure program for performing SCF- and
	  MCSCF-gradient calculations, together with a variety of
	  techniques for post Hartree Fock calculations. 
	- version ?, written in ?
	- http://gserv1.dl.ac.uk/CCP/CCP1/gamess.html

=======
stuff from ncbi

database searching tools (for remote database queries)

the ncbi package...

linux binary of the network database search tools:
ftp://ncbi.nlm.nih.gov/blast/network/blast2/
this includes blastp, blastn, tlbastn, tblastx etc.  works like a
charm under cron control for regular database searching...

this requires the network Entrez program to be configured, get a linux
binary here:  ftp://ncbi.nlm.nih.gov/entrez/network/linux.tar.Z

=======
sequin	- ncbi's "new" sequence submission/editing tool
	- version ?, written in C
	- ftp://ncbi.nlm.nih.gov/sequin/linux.tar.Z
	- http://www.ncbi.nlm.nih.gov/Sequin/index.html

this compiles and runs just fine on my system.

=======
fasta	- database search tool
	- version ?, written in C
	- ftp.virginia.edu/pub/fasta/fasta30t6.shar.Z

used default makefile but changed THR_CC= to be blank then 'make
sall'. 
=======
RNA folding related software:

Viena RNA package - various calculations of RNA structure
	- version 1.1b, written in C
	- ftp://ftp.itc.univie.ac.at/pub/RNA/ViennaRNA-1.1b.tar.gz 

compiles fine under Linux but Makefile needs tweaking (hell, i managed
to get it to work...)

=======
naview	- An improved algorithm for the display of nucleic acid
	  secondary structures 
	- version ?, written in C
	- ftp://snark.wustl.edu/pub/naview.tar.Z
	- http://www.ibc.wustl.edu/~zuker/ref/BRUR88.html

this compiles fine under Linux but i haven't used it.

=======
SeqPup - sequence editor and analysis program.  includes links to
	 network services and external analysis programs.
	- version ?, written in C, binary provided
	- ftp://iubio.bio.indiana.edu/molbio/seqpup/
	  unix/linux-i86-elf/
	- ftp://iubio.bio.indiana.edu/util/dclap/source/

does not seem completely stable...

=======
tacg	- restriction site analysis program
	- version ?, written in C
	- ftp://mamba.bio.uci.edu/pub/tacg/

works on plain text files with sequence in them...

source code compiled fine.  the provide binary in the bin dist is
a.out (QMAGIC).

=======
SignalScal - scan for transcription factor binding sites
           - version 4.07, written in C, compiles fine
           - ftp://biosci.umn.edu/pub/sigscan/unix

this works great on my system...
it's a good idea to read this file:
ftp://biosci.umn.edu/pub/sigscan/unix/readme.unix 

=======
PIMA	- pattern induced multiple sequence alignment
	- version 1.40, written in C, compiles fine
	- ftp://gc.bcm.tmc.edu/pub/software/pima

ftp://gc.bcm.tmc.edu/pub/software/pima/README

passes builin tests just fine after compilation.

=======
Predator - structural prediction based on multiple alignments
	 - version 1.0, written in C, compiles fine
         - ftp://ftp.ebi.ac.uk/pub/software/unix/predator

output on my Linux box was identical to output on an SGI using the
precompiled binary for IRIX and the binary i compiled.

=======
ClustalW - pairwise and multiple alignments
         - version 1.60, written in C, compiles fine
         - ftp://ftp.ebi.ac.uk/pub/software/unix

tested it, works fine on my Linux system.

=======
Seqsee - protein sequence analysis package
       - version 1.2, written in C, compiles fine
       - available upon request from
	 seqsee at procyon.biochem.ualberta.ca


=======
Pratt	- pattern discovery in sets of unaligned sequences
	- version 2.0, written in C, minor changes
	- ftp://ftp.ii.uib.no/pub/bio/Pratt/Pratt2.tar
	- http://www.ii.uib.no/~inge/Pratt.html

this segfaults but only apparently after a run has finished.
otherwise appears ok...

=======

Primer3 - PCR primer design
        - release 0.1, written in C, compiles fine
        - ftp://genome.wi.mit.edu

all tests passed just fine on my system.

=======
GDE	- genetic data environment
	- release ?, written in ?
	- gopher://megasun.bch.umontreal.ca:70/11/GDE/ 

binaries are a.out (ZMAGIC), requires (a.out) xview libraries. 
i tried to compile this myself but not very hard - it wouldn't work.

==============================================================================


- -- 
"Those that give up essential liberty to obtain a little temporary
 safety deserve neither liberty nor safety." -- Benjamin Franklin (1773)
			  finger for PGP key
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