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Table 5 Comparison of tools considering compatible network file formats exporting.

From: Visualization of protein interaction networks: problems and solutions

File Format

Tools

 

Arena3D

AVIS

BioLayout3D

Cytoscape

Medusa

NAViGaTOR

ONDEX

Osprey

Pajek

PIVOT

ProViz

BioPAX

-

-

-

-

-

-

-

-

?

?

txt

-

-

-

-

?

?

SIF

-

-

-

-

-

-

-

?

?

xml

-

-

-

-

-

-

-

?

?

html

-

-

-

-

-

-

-

-

?

?

XGMML

-

-

-

-

-

-

-

?

?

png

-

-

-

-

?

?

bmp

-

-

-

-

-

-

?

?

jpg

-

-

-

?

?

pdf

-

-

-

-

-

-

-

?

?

eps

-

-

-

-

-

?

?

svg

-

-

-

-

-

?

?

tiff

-

-

-

-

-

-

-

-

?

?

GIF

-

-

-

-

-

-

-

-

?

?

GML

-

-

-

-

-

-

-

-

?

?

VizMap

-

-

-

-

-

-

-

?

?

net

-

-

-

-

-

?

?

  1. The table lists the file formats that each tool is able to export starting from the visualized produced graph. Analyzing this table, it is possible to note that there exist a lot of different file formats, but each tool is able to save file in a limited number of different formats. More information on the save/export functions can be found in the tool's website, cited in the previous section. The ? means that it was not possible to establish the feature for the tool.
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BMC Bioinformatics

ISSN: 1471-2105

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