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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/pimaftp://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
zifi runs LINUX 2.1.1 -=-=-=WEB=-=-=-> http://zifi.genetics.utah.edu
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