I dunno... It looks more like an AI problem than a perl problem. What's the metric you use to determine 'sameness'? And, are the groups 'real' (ie have defined value/property independent of strains) or just buckets to put things in if they are different enough from others?

My inclination would be to use numerical methods (eg principal component analysis) first. But I'm speaking as a biologist, not a perlie.