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 |
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 |
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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