SPNConverter 1.0 – Tool to Convert Graphs into GraphML Format

SPNConverter 1.0

:: DESCRIPTION

SPNConverter enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language (SBML) to Graphml format.

::DEVELOPER

Group of Clinical Genomic Networks

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • CytoScape
:: DOWNLOAD

 SPNConverter

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Oct 1;29(19):2507-8. doi: 10.1093/bioinformatics/btt421. Epub 2013 Aug 1.
SPNConverter: a new link between static and dynamic complex network analysis.
Dent JE1, Yang X, Nardini C.

Fitchi – Haplotype Genealogy Graphs based on Fitch Distances

Fitchi

:: DESCRIPTION

Fitchi is a python script that produces haplotype genealogy graphs from alignment files in Nexus format, along with summary statistics.

::DEVELOPER

EVOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Fitchi

:: MORE INFORMATION

Citation

Fitchi: Haplotype genealogy graphs based on the Fitch algorithm.
Matschiner M.
Bioinformatics. 2015 Dec 9. pii: btv717.

CorNet 2.01 – Correlation Network Graphs

CorNet 2.01

:: DESCRIPTION

 CorNet is a R-script largest correlation network graphs for visualizing clusters of intercorrelated genes/transcripts

::DEVELOPER

Bioinformatics at AWI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R Package

:: DOWNLOAD

 CorNet

:: MORE INFORMATION

Citation

Hüning AK, Melzner F, Thomsen J, Gutowska MA, Krämer L, Frickenhaus S, Rosenstiel P, Pörtner HO, Philipp E, Lucassen M
Impacts of seawater acidification on mantle gene expression patterns of the Baltic Sea blue mussel: implications for shell formation and energy budget. (2012),
Marine Biology . August 2013, Volume 160, Issue 8, pp 1845-1861 doi: 10.1007/s00227-012-1930-9

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