A couple of applications are now available for visualizing flows through geographic space. This is especially useful for research that combines GIS and Network Analysis.
CSISS - Spatial Tools: Tobler's Flow Mapper is a stand-alone program that is relatively easy to learn and use.
An ARC GIS add on program authored by Alan Glennon (of UCSB), while not as user-friendly or accessible as the Tobler program, allows for making more sophisticated maps.
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