I see that you have gone with a distance measurement. When doing this a while back, we included correlations as well. So you could look at the data either as a function of a measurement (distance) or a statistical (correlation coeficient for parametric and Spearman Rank Correlation for non parpametric analysis). Perhaps you could think about allowing the algorithm to use either metric or statistical methods to increase the module's utility at some point. If you look on CPAN you'll find Statistics::RankCorrelation. If you would like to calculate your distances outside of your module, there is Math-NumberCruncher. Mind you I could find nothing on Tschebyschev in CPAN though.
MadraghRua
yet another biologist hacking perl....
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