how to read a hierarchical tree

Question

[silvia.caprari84]

Hi all,

I have some hierarchical trees represented by dendrograms as a results of the server Procksi on some of my proteins (I wanted to see if any structural similarities among them). My question is from which level of branching of the tree is it better to start considering a "cluster"? from first ramification?second? I mean..from which level you generally start distinguishing the different groups? I read that generally a cut-off is used, but I am not sure to have understood well what it means and how I can use it and if I have to use another tool to cut the tree. Furthermore, how I choose the value of cut-off?

Thank you very much.

Silvia