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I have a graph file (in DOT format, as well as SVG) containing thousands of nodes and edges. All the nodes and edges have different labels etc.

It is difficult to comprehend and find the information just by looking at it in a viewer. Sometimes I'd like to follow an edge to another node but on its way it would merge with many other congested edges making it difficult to trace. And other times, I'd like to simply filter out edges or nodes based on some search criteria, or just filter out neighboring nodes.

Is there any tool well suited for this task? I tried using Gephi but couldn't accomplish what I'd like to do; I found its layouting and node labelling far inferior compared to simple DOT to SVG conversion.

I am open to using any platform: Mac, Ubuntu or Windows but Mac & Ubuntu solutions are preferred.

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script / program your own parser from scratch or with perl, python, java, C libraries for graphviz. –  Ярослав Рахматуллин Dec 9 '12 at 15:36

2 Answers 2

I'm surprised Gephi didn't work for you. There are other tools in the same vein that provide an interactive view of a graph and various filters.

Cytoscape is a Java interactive graph exploration tool like Gephi, but targeted at biologic networks.

NodeXL would be the most flexible alternative. It is a FOSS template for Excel 2007--2013 that will load a graph into tables of an Excel workbook then display the graph in a separate interactive pane. There is brushing and linking between the views, and you can even edit the graph in the workbook. It provides a set of filters based on any data columns you have, as well as any graph statistics you calculate like degree, betweenness centrality, clusters, etc. Because it is in Excel, you can write custom formulas or macros to select rows to filter too. Here is an example image:

NodeXL showing senate voting patterns

Disclaimer: I am an advisor on the NodeXL project.

By the way, if you are trying to convert your DOT file to the formats these other tools can read you can use something like NetworkX for the conversion. Here is the specific method you need.

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I have no idea if Graphviz will solve your problem but I guess it couldn't hurt to load your DOT file into it and see what it can/can't do for you. It has a version for Win/Mac/Linux.

http://www.graphviz.org/

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GraphViz is one of the layout engines supported by Gephi. –  reinierpost Sep 4 at 16:25

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