Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Misc

[http://sbw.kgi.edu/research/sbwIntro.htm Systems Biology Workbench]

BSD

vital

not trivial?

no

Networks

[https://networkx.lanl.gov/ NetworkX]

(L)GPL

depends on python

free

no

Graphical representation of networks

[http://atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html ?PhyloGrapher]

GPL

depends on Tcl/Tk

free

no

Graph visualisation

[http://www.gravisto.org/ gravisto]

GPL

depends on java

free

no

Motif analysis and visualistion

[http://mavisto.ipk-gatersleben.de/ mavisto]

GPL

depends on java, based on gravisto

free

no

Networks

[http://cneurocvs.rmki.kfki.hu/igraph/ The igraph library]

GPL

[http://cneurocvs.rmki.kfki.hu/igraph/debian unofficial Ubuntu packages]

free

no

Networks

[http://www.boost.org/libs/graph/doc/index.html The Boost Graph library]

BSD

[http://packages.debian.org/unstable/source/boost main]

free

no

Networks

[http://angel.elte.hu/clustering/ CFinder]

free for academics, but strange phrasing

java program

no

Networks

[http://erzuli.ss.uci.edu/R.stuff/ Social Network Analysis Tools]

GPL

depends on R

free

no

Motif detection in networks

[http://www.minet.uni-jena.de/~wernicke/motifs/ FANMOD]

Academic

depends on [http://cs.anu.edu.au/~bdm/nauty/ nauty]

no

Things related to Gene Ontology and offspring:

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Comparison

[http://gutsc.wustl.edu/GOurmet/ GOurmet]

BSD

depends on Java

new

no


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