I've worked with fairly large graphs in connection with Y2K analysis.
I used GraphViz for a start, but increasingly switched to yED
for faster generation, more flexible and interactive layout, graph partitioning and analysis, -- and more.
There's no Perl interface to yED, but it's simple (in Perl :) to generate the raw graph data files
or a 'free form' XML & XSLT format of your choice.
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