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

[http://www.gene.com/share/gmap/ GMAP]

no profit, no redistribution of modified versions

impossible?

no

Whole-genome alignments

[http://mummer.sourceforge.net/ mummer]

Artistic

make failed

[http://bugs.debian.org/201761 RFP]

no

Comparative genomics

[http://lagan.stanford.edu/lagan_web/index.shtml Lagan]

GPL

[https://www.bioinformatics.uwaterloo.ca/wiki/index.php?Lagan private repository]

free

no

Comparatige genomics

[http://www.microbialgenomics.org/BSR/ BSR]

[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

[http://baboon.math.berkeley.edu/mavid/ MAVID]

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

[http://genome.jouy.inra.fr/MuGeN/ MuGeN]

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/LICENSE.txt MLX]

[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

[http://www.inrialpes.fr/helix/people/viari/genepi/ Genepi]

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

[http://sourceforge.net/projects/aped/ APED]

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

[http://www.cs.wustl.edu/~jbuhler/dapple/ Dapple]

GPL

depends on Qt, FFTW

free

no

Clustering

[http://sourceforge.net/projects/gedas gedas]

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

[http://depts.washington.edu/l2l/ L2L]

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

[ftp://ftp.tuebingen.mpg.de/ebio/protevo/TPRpred/ TPRpred]

GPL

looks easy

free

no

Repeat finding

[http://www.drive5.com/pilercr/ PILER]

Public domain

looks easy

free

no

Repeat masking

[http://www.ii.uib.no/~ketil/bioinformatics/tools.html RBR]

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

[http://zeus.cs.vu.nl/programs/trustwww/ TRUST]

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]

[http://www.broad.mit.edu/wga/license_reg.html Academic]

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

[http://www.bcgsc.ca/bioinfo/software/FASSI FASSI]

GPL

trivial

free

no

BAC scaffolding

[http://www.agcol.arizona.edu/software/fpc/ fpc]

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

[http://www.in-machina.com/~reece/autoseq/ autoseq]

Public domain

Old C++ which may not be compatible with recent gcc

free

no

Band calling

[http://www.sanger.ac.uk/Software/Image/ Image]

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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