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As i wrote directly to to Mark, I'm sending comments to list.

> what software do you use to do this?

Graphviz and perl module.

> what is the meaning of a directed line from one node to another?   
> (e.g. communication in the direction
> of the arrow, or controlled by the thing the arrow points to...)

If c&c domain use more IP, then there exists more edges to it. If
another different c&c domain use any from matched IP's, then 
another edge span another group of IP's in this c&c, etc..

> is there any way to make this searchable?

Not directly.

> is there any way to try to cluster the machines which are close  
> together (using any metric) to be physically close together?
> i'm not sure what metrics you might want to use.  possibly just "in  
> the same AS".

It's good idea for future.


Btw: Here is small circle view, maybe better for quick structure
corelation.

http://www.honeynet.cz/img/small-circo.jpg





Cheers

David Vorel

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