CytoGEDEVO

Pairwise global alignment of PPI or other networks
CytoGEDEVO is a tool for visual and human-assisted network alignment. It aligns pairs of networks, where the result is a one-to-one node mapping. Alignments are fully resumable, i.e. parameters can be adjusted anytime and the alignment resumed with the new parameters. Expert knowledge can be incorporated by the user by fixating node pairs. CytoGEDEVO is not limited to network topology and can make use of an unlimited number of externally supplied scores, without imposing restrictions on the score type (that means you can just throw BLAST E-values or Bit-scores or whatever at it and it will work). Also allows importing result files generated by other aligners. Command-line versions are available on our website. **Note:** CytoGEDEVO runs on Windows, Linux, and Mac OSX; both x86 and x64. If you need support for other operating systems or architectures, ask. If you encounter any issues or bugs, please report them on our [bug tracker](https://bitbucket.org/maxmalek/cytogedevo/issues). Citation: *Malek M, Ibragimov R, Albrecht M, Baumbach J (2015) CytoGEDEVO - Global alignment of biological networks with Cytoscape. Bioinformatics. 2015 (in press).* [[link](http://bioinformatics.oxfordjournals.org/content/early/2015/12/14/bioinformatics.btv732)]

1.0.3.1

Works with Cytoscape 3.0

Release Notes

- Fix possible ConcurrentModificationException when pressing coloring preset button, resulting in task failure - Fix possible NullPointerException here and there - (No changes to the C++ side this time) Bug tracker opened: https://bitbucket.org/maxmalek/cytogedevo/issues -- Please report issues there!

1.0.3

Works with Cytoscape 3.0

Release Notes

- Fix possible endless loop in directed mutation for very small networks with prematched nodes under some circumstances - Fix custom matrix order in UI (was reversed) - Allow changing custom matrix order via UI - Attempt to fix sporadic/random failure in quick coloring buttons (esp. CCS) - Allow exporting only selected nodes into alignment file

1.0.2

Works with Cytoscape 3.0

Release Notes

* Fixed typo that caused similarity matrices to be normalized wrongly when clamp or rescale mode was used, resulting in garbage alignment. (Note: Distance matrices worked fine!) * Ensure the "toggle mapping mode" button is clearly recognizable as active even under a horribly flat UI such as win8.

1.0.1

Works with Cytoscape 3.0

Release Notes

fixed failure to load data matrix file under some circumstances if numbers were scientific notation formatted. Affects at least windows x64. Linux (both archs) and windows x86 seemed to work fine. Not sure about OSX.

1.0

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.0.3.1

License Click here

Released 19 Oct 2015

Works with Cytoscape 3.0

Download Stats Click here