6436
Comment: Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format
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6572
Cluster Database at High Identity with Tolerance
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||Database clustering||[http://bioinformatics.org/cd-hit/ CD-HIT]||Not found, but homepage says open source||Straighytforward|| ||no|| |
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 |
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 |
|
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 |
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 |
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 |
|
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 |
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 |
Visualisation |
[http://jtreeview.sourceforge.net/ Java ?TreeView] |
GPL |
[http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/treeview/ unofficial] |
free or contrib ? |
yes |
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Repeats
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
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 |
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
Genome assembling
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
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 |
|
Assembling |
[http://sourceforge.net/projects/wgs-assembler/ Whole Genome Assembler] |
GPL |
|
free |
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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