(Maybe) future Debian-Med packages
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Hi
As Andreas Tille said to me, I am posting here some bioinformatic programs.
CARA: Computer Aided Resonance Assignment
Homepage: http://www.nmr.ch/
License: Free (none specified). In the future will be released under
Sleepycat license.
Upstream author allowed to distribute, but since it's available only in
a pre-compiled form (no source code), it can't go on Debian. He also
said that when he will release the sources in the future.
FASTA: Compares a protein sequence to another protein sequence or to a
protein database, or a DNA sequence to another DNA sequence or a DNA
library.
Homepage: http://fasta.bioch.virginia.edu/
License: Unknown
Upstream author don't allow to distribute source code or a binary
package, but he permits to distribute a script to download FASTA,
compile and install. I don't know if it can go on Debian.
gdpc: is a program for visualising molecular dynamic simulations, it is
a very versatile program and could easily be used for other purposes.
gdpc reads xyz input and custom formats and can write out pictures of
the frames.
Homepage: http://koti.welho.com/jfrantz/software/gdpc.html
License: GNU GPL
gff2aplot: Pair-wise alignment-plots for genomic sequences in PostScript.
Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html
License: GNU GPL
gff2ps: Produces PostScript graphical output from GFF-files.
Homepage: http://genome.imim.es/software/gfftools/GFF2PS.html
License: GNU GPL
AcE: Gene finding accuracy evaluation
Homepage: http://bioinformatics.org/project/?group_id=39
License: GNU GPL
geneid: program to predict genes in anonymous genomic sequences designed
with a hierarchical structure.
Homepage: http://genome.imim.es/software/geneid/index.html
License: GNU GPL
sgp2: program to predict genes by comparing anonymous genomic sequences
from two different species
Homepage: http://genome.imim.es/software/sgp2/index.html
License: GNU GPL
Gromcas: GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with
hundreds to millions of particles.
Homepage: http://www.gromacs.org/features/index.php
License: GNU GPL
There is an ITP (#228319 and #252101). Packages available at
http://magnet.ofb.net/debian/
Mummer: system for rapidly aligning entire genomes, whether in complete
or draft form.
Homepage: http://www.tigr.org/software/mummer/
License: Original Artistic License (I asked upstream, since there was a
doubt about that).
There is a RFP open (#201761).
nmrview: Software for the Visualization and Analysis of Nuclear Magnetic
Resonance Data
Homepage: http://www.onemoonscientific.com/nmrview/
License: Free. None specified.
There is a C version unsupported and a new one, in Java. Must
investigate it upstream allow to distribute.
raster3d: set of tools for generating high quality raster images of
proteins or other molecules.
Homepage: http://www.bmsc.washington.edu/raster3d/raster3d.html
License: Free, but withou license.
Upstream author allow me to distribute. I think that if it go on Debian,
it would be on non-free. (I can put what upstream said, if someone wants).
sim4: a program to align cDNA and genomic DNA
Homepage: http://globin.cse.psu.edu/html/docs/sim4.html
License: GNU GPL
spscan: supports semi-automatic assignment of NMR spectra of biological
macromolecules.
Homepage: http://gaudi.molebio.uni-jena.de/~rwg/spscan/
License: GNU GPL
t-coffe: Multiple local sequence alignment
Homepage:
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
License: Academic License (???)
There is an open ITP with more than 1 year (#205370). I have talked to
upstream author and he said that the next version is under heavy
development and will be released under GNU GPL.
wise2: package that is focused on comparing DNA sequences at the level
of its conceptual translation, regardless of sequencing error and introns.
Homepage: http://www.ebi.ac.uk/Wise2/
License: GNU GPL
There is a RFP open (#200591).
Smile: Find statistically significant patterns in sequences
Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
License: GNU GPL
Debian package available at http://tp12.pzr.uni-rostock.de/~moeller/debian/
Open ITP (#221492).
ammp: full-featured molecular mechanics, dynamics and modeling program.
Homepage: http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html
License: Unknown (I am veryfying)
Softwares that I have asked for permission but they said "It's a good
idea, but I won't allow because I can't know if your version is the same
of our version", "Yes, we allow but since the software has parts that
are owned by company XYZ, you have to aske them" (company XYZ is
commercial and didn't allow) or even a "No." :-)
Since they can't be redistributed, I won't make a long description.
CCP4 (www.ccp4.ac.uk)
CNS (http://cns.csb.yale.edu/v1.0/)
Modeller (http://salilab.org/modeller/)
Molmol (http://hugin.ethz.ch/wuthrich/software/molmol/index.html)
Xplor-NIH (http://nmr.cit.nih.gov/xplor-nih/)
Xtalview (http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html)
I think that might be more... I don't remember right now.
Some programs I have packed, but since when I created the package I was
still a beginner (well, I am still one :-P ), I will have to redo the
packages. I see no problem on this.
Thanks
Cheers,
Nelson
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