[BiO BB] Clade designation/clustering

[Burke Squires]

Hello all,

I am characterizing strains of an organism and trying to distinguish  
clades of individual genes. I have performed multiple sequence  
alignments, created phylogenetic trees and done distance matrix  
calculations. I can "see" clades in the tree but I want to  
statistically prove that they are clades. How do I do this? I have  
tried some hierarchical clusterings but maybe I do not have the right  
program. Got any ideas?

Thanks,

Burke