Analysis of network structure

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Clustering of graphs

MCL

GPL

packaged ([http://packages.debian.org/mcl main])

no

Implementation of Girvan and Newman's algorithm

[http://www.cs.ucr.edu/~qyang/software.html PEBC]

GPL

depends on LAN/MPI and Boost

free

no

Implementation of Clauset et al's algorithm

[http://www.cs.unm.edu/~aaron/research/fastmodularity.htm FastCommunautyMH]

GPL

trivial

free

no

Local clustering of expression vectors

[http://research.stowers-institute.org/bioinfo/software/psi-square/index.html psi-square]

Academic

maybe impossible because of one needs to register first

no

Finding cliques in a network

[http://users.tkk.fi/~pat/cliquer.html Cliquer]

GPL

Did not figure out if it is a library

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

Calculation and visualisation of centralities

[http://centibin.ipk-gatersleben.de/index.php CentiBIN]

free of charge

java program with unclear licence

no

Visualisation

[http://brak.sdsc.edu/pub/BiologicalNetworks/index.php ?BiologicalNetworks]

Not found

depends on Java

no

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Representation of networks

Program

Licence

Packaging

Importance

Listed on microbio.wml?

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

BSD

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

no

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

GPL

depends on Tcl/Tk

free

no

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

GPL

depends on java

free

no

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

CPLv1

packaged ([http://packages.debian.org/unstable/graphics/graphviz.html main)]

no

[http://www.chaosreigns.com/code/springgraph/ springgraph]

GPL

packaged ([http://packages.debian.org/unstable/graphics/springgraph main])

no

[http://cbi.labri.fr/eng/proviz.htm ?ProViz]

depends on tulip

no

[http://biodata.mshri.on.ca/osprey/ Osprey]

Academic

requires specific authorisation

no

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Gene Ontology

[http://geneontology.sourceforge.net/ Gene Ontlolgy]

Artistic

Some depend on perl, some on java

free

no

Using GO with perl

[http://search.cpan.org/dist/GO-TermFinder/ GO::?TermFinder

MIT

cpan module

free

no

Comparison

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

BSD

depends on Java

new

no

In addition, there is a [http://www.geneontology.org/GO.tools.microarray.shtml long list of tools] for microarray analysis on the GO website.

Others

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Networks

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

GPL

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

free

no

Machine learning for data mining tasks

[http://www.cs.waikato.ac.nz/ml/weka/ WEKA]

GPL

depends on java

no

Multipurpose

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

BSD

not trivial?

free

no

Multipurpose

[http://jung.sourceforge.net/ JUNG]

BSD

depends on java

free

no

Network data storage and manipulation

[http://www.ebi.ac.uk/intact/index.jsp ?IntAct]

Apache

depends on Java

free

no

Networks

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

(L)GPL

depends on python

free

no

Motif analysis and visualistion

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

GPL

depends on java, based on gravisto

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

Extrapolate a network from expression and genome data

[https://bioinformatics.cs.vt.edu/xcisclique/ ?XcixClique]

GPL

depends on matlab

contrib?

no

Inferring transcriptional module networks

[http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Information_Lemmens_2006/Index.html ?ReMoDiscovery]

LGPL

depends on java

free

no

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?


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