This doesn't sound like it's a question of software. You need some appropriate research design and statistical method which you can use to do what you're trying to do; once you know what statistical method you need, then you can try to think about which statistical software implements that method. If it's a common method, it will be implemented in any software package.

Try pls

Distance software

Sigmastat software

CANOCO 5.0 is available :http://www.canoco5.com/index.php/canoco5-overview