Short explanation:
This page lists programs which are usefull to the field of Genomics. It is mostly software related to microarrays, genome sequencing, and whole-genome analysis.
Most column names are self-explanatory. When a licence is listed as "Academic", it means that the program is only free of charge for academic, non-profit research, which makes non-compliant to the DebianFreeSoftwareGuidelines. "Packaging" gives cues about the difficulty of the packaging, or indicates that the program has already been packaged. "Importance" gives cues about what to package first. That is why programs already packaged have nothing written there: it does not mean that they are not important!. "Listed on... " records whether the program is listed on the official DebianMed website.
Unsorted
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
RNA mapping |
no profit, no redistribution of modified versions |
impossible? |
|
no |
|
Whole-genome alignments |
[http://mummer.sourceforge.net/ mummer] |
Artistic |
make failed |
no |
|
Comparative genomics |
GPL |
[https://www.bioinformatics.uwaterloo.ca/wiki/index.php?Lagan private repository] |
free |
no |
|
Comparatige genomics |
[http://www.microbialgenomics.org/BSR/BSR_README.txt non-free] |
Prior agreement required |
|
no |
|
Genome Browser |
[http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513 Generic Genome Browser] |
Artistic |
maybe not easy |
Academic ones are really expensive for commercial use |
no |
Genome Browser |
[http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html ?OmicBrowser] |
GPL |
depends on java |
flash plugin required for use |
no |
Integrated environment |
[http://sourceforge.net/projects/gmod/ Generic Model Organism Database (GMOD)] |
Artistic |
complex |
important |
no |
Genome database |
[http://www.acedb.org/ acedb] |
(L)GPL |
maybe not easy |
some programs depend on acedb libs |
no |
Prophage detection in prokaryotes |
[http://phage-finder.sourceforge.net/ Phage_Finder] |
GPL |
Depends on perl, ncbi-blast, some perl modules, xgraph, trnascan, and others |
free |
no |
Database schema |
[http://fuge.sourceforge.net/ FuGE] |
not found |
xml schema |
|
no |
Generic database framework |
[http://www.gusdb.org GUS] |
BSD |
depends on java and perl |
Used by many databases |
no |
Manipulating gff files |
[http://biowiki.org/GffTools gffTools] |
no licence |
lot of manpages to write! |
|
no |
Multiple alignments |
academic |
would depend on clustalw and fastdnaml |
|
no |
|
EST clustering |
[http://www.ii.uib.no/~ketil/bioinformatics/tools.html xsact] |
not found |
Haskell program, did not build on ppc |
|
no |
Discovery of regulatory regions |
[http://www.cs.helsinki.fi/u/kpalin/EEL/ Enhancer Element Locator] |
GPL |
depends on pytohon |
free |
no |
genomic sequence analysis tools |
[http://sourceforge.net/projects/cartwheel Cartwheel Bioinformatics Package] |
GPL+LGPL |
doesn't seem difficult |
|
no |
Genetic maps |
[http://carl.agtec.uga.edu/MapMerger/ ?MapMerger] |
no licence |
php cgi |
|
no |
Database of SAGE tags |
[http://pbil.univ-lyon1.fr/software/identitag/ identitag] |
not found |
perl and sh scripts |
|
no |
Codon usage analysis |
[http://codonw.sourceforge.net/ CodonW] |
GPL |
maybe easy |
free |
no |
Visualisation of annotations |
Not found |
Depends on gtk, xml, dbi, bioperl, ... |
|
no |
|
SNP analysis |
[http://www.bioinformatics.nl/tools/snpweb/ QualitySNP] |
GPL |
C program plus website |
free |
no |
Gene predicion |
[http://analysis.ccgb.umn.edu/diogenes/ Diogenes] |
Not found |
./configure && make fails, but it seems easy to fix |
|
no |
Rearrangements analysis |
[http://www.cs.unm.edu/~moret/GRAPPA/ Grappa] |
GPL |
straightforward |
free |
no |
Clustering analysis (+GUI) |
[http://woldlab.caltech.edu/compClust/ compClust] |
[http://woldlab.caltech.edu/compClust/debian_install.shtml unofficial package] |
Did not check if the license is DFSG-free... |
no |
|
Database clustering |
[http://bioinformatics.org/cd-hit/ CD-HIT] |
Not found, but homepage says open source |
Straighytforward |
|
no |
cis-regulatory element analysis |
[http://cistematic.caltech.edu/ cistematic] |
MIT |
depends on python and sqlite |
free |
no |
Gel analysis |
[http://www.proweb.org/gelbuddy ?GelBuddy] |
[http://www.proweb.org/gelbuddy/download.html Academic with invariant sections] |
Depends on java |
Will not be packaged unless requested |
no |
Gene structure annotation and analysis |
[http://pasa.sourceforge.net PASA] |
Artistic |
C++, Perl |
|
no |
Annotation |
LGPL |
depends on Java |
free |
no |
|
Gene finding in prokaryotes |
[http://www.cebitec.uni-bielefeld.de/groups/brf/software/gismo gismo] |
GPL |
Depends on bioperl, python, hmmer, and libsvm |
free, complex dependancies |
no |
Align expressed and genomic sequences |
[http://sibsim4.sourceforge.net/ SIBsim4] |
GPL |
C |
rewrite of sim4 |
yes |
Gene prediction (through GHMM) |
[http://www.genezilla.org/ ?GeneZilla] |
Artistic |
C++ |
state-of-art |
no |
Analysis of high-throughput data |
Artistic |
Depends on Java and Perl |
free |
no |
|
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Microarrays
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Suite |
[http://www.tm4.org/ TM4] |
artistic |
depends on java |
free |
no |
Suite |
[https://launchpad.net/asterias asterias] |
GNU and Affero GPL |
Depends on webserver, R, and python |
free |
no |
Microarrays |
[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1540 SNOMAD] |
GPL |
depends on R |
free |
no |
Microarrays |
[http://genopolis.btbs.unimib.it/genopolis/material/mattia/private_mattia.htm amda] |
GPL |
R package depending on bioconductor |
free |
no |
Image analysis for microarrays |
GPL |
depends on Qt, FFTW |
free |
no |
|
Clustering |
GPL |
depends on QT4 |
free |
no |
|
Microarrays |
[http://db.systemsbiology.net/software/VERAandSAM/ Vera, Sam] |
not found |
looks easy |
|
no |
Normalisation |
[http://www.transcriptome.ens.fr/goulphar/ Goulphar] |
GPL |
R module depending on Bioconductor |
free |
no |
Genome-scale oligonucleotide design |
[http://berry.engin.umich.edu/oligoarray2_1/ ?OligoArray 2.1] |
GPL |
Depends on Java |
free |
no |
Comparison between experiments |
GPL |
Depends on perl |
free |
no |
|
False Discovery Rate |
[http://www.stjuderesearch.org/depts/biostats/fdrlibrary/index.html FDRlibrary] |
not found |
R library |
|
no |
False Discovery Rate |
[http://www-stat.stanford.edu/~tibs/SAM/Rdist/index.html samr] |
LGPL |
R library |
free |
no |
Combining Batches |
[http://www.biostat.harvard.edu/~wjohnson/ComBat/ComBat.html ?ComBat] |
Not found |
R script |
|
no |
Visualisation |
[http://jtreeview.sourceforge.net/ Java ?TreeView] |
GPL |
[http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/treeview/ unofficial] |
free or contrib ? |
yes |
Submission to ?ArrayExpress |
[http://sourceforge.net/projects/tab2mage tab2MAGE] |
Apache |
Depends on Perl. Would provide libarrayexpress-perl? |
free |
no |
Submission to MIAMExpress |
[http://sourceforge.net/projects/miamexpress/ miamexpress] |
Contains an acknowledgement clause |
Depends on Apache, Perl-CGI and MySQL |
maybe non-DFSG-free |
no |
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Repeats
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Repeat finding |
GPL |
looks easy |
free |
no |
|
Repeat finding |
[http://www.drive5.com/pilercr/ PILER] |
Public domain |
looks easy |
free |
no |
Repeat masking |
Not found |
[http://www.ii.uib.no/~ketil/bioinformatics/tools.html unfficial] |
|
no |
|
Repeats analysis |
[https://nbcr.sdsc.edu/euler/ ?RepeatGluer] |
Not found |
straightforward |
|
no |
Repeat finding |
[http://repeatscout.bioprojects.org/ ?RepeatScout] |
Not found |
straightforward |
|
no |
Repeat finding |
not found |
Depends on java and [http://catcode.com/pngencoder/ pngencoder] (LGPL) |
|
no |
|
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Genome assembling
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Assembling |
[http://sourceforge.net/projects/wgs-assembler/ Whole Genome Assembler] |
GPL |
|
[http://bugs.debian.org/395843 RFP #395843] |
no |
Assembling |
[http://www.tigr.org/software/assembler/ TIGR Assembler] |
OSI-certified |
|
free |
no |
Assembling |
[http://amos.sourceforge.net/ amos] |
Artistic |
depends on Perl and Qt |
free |
no |
Assembling |
[http://www.phrap.org/ phrap] |
commercial product open only to registered academics |
depends on Perl |
not redistributable |
no |
Assembling |
[http://www.broad.mit.edu/wga/ Arachne] |
|
non-free |
no |
|
Assembling |
[http://www.hgsc.bcm.tmc.edu/downloads/software/atlas/ Atlas] |
[http://www.hgsc.bcm.tmc.edu/downloads/software/atlas/license.html Academic] |
depends on phrap |
non-free |
no |
BAC scaffolding |
GPL |
trivial |
free |
no |
|
BAC scaffolding |
Academic |
|
|
no |
|
Base calling |
[http://www.broad.mit.edu/ftp/distribution/software/Bass/ bass] |
BSD with advertising clause |
Does not compile out of the box |
|
no |
Base calling |
Public domain |
Old C++ which may not be compatible with recent gcc |
free |
no |
|
Band calling |
unknown |
did not find the sources |
|
no |
Clustering
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Clustering of SAGE expression |
[http://www.bcgsc.ca/bioinfo/ge/treebuilder/ TreeBuilder3D] |
GPL |
depends on java |
|
no |
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