Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
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 |
Integrated environment |
[http://sourceforge.net/projects/gmod/ Generic Model Organism Database (GMOD)] |
Artistic |
complex |
important |
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 |
|
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 |
Microarrays |
[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1540 SNOMAD] |
GPL |
depends on R |
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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