I've been using Pajek for about four years now. It is robust with
well-maintained user manuals.
You can download it from http://vlado.fmf.uni-lj.si/pub/networks/pajek/
The file format is simple; you can manually input an adjacency matrix
(I tend to use Excel and then save as a text file) or Sheep wrote an
Axman or Meanda (I must check which) to Pajek exporter. We tried this
with London and it handled 16000 lines without any problem! (And you
could "spin" the 3d graph when you were finished).
It can then do a number of very interesting visualizations and
computations. Amongst other things you can do are:
automatic justified graphs
shortest path calculations
various cluster analyses
energy diagrams
and many many more things, far more complex than our usual
requirements. And it's so easy that I've taught it to students for
the last couple of years.
Oh, and it's free!
Ruth
ps- you can view some of my student's graphs on
http://undertow.arch.gatech.edu/homepages/rdalton/MUD/coursework.htm
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