Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

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

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

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

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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