phylogenetic trees

[marcvdc at lmb1.rug.ac.be]

Dear Netters,


I have problems with generating a nice phylogenetic tree in the sense that the 
tree is not correct. How is my tree made :

1) multiple sequence alignment 
    of the proteins with the program "PILEUP" in GCG gives an msf-file. The 
    alignment is at first view o.k.  The proteins I use belong to a protein 
    family which should be subdiveded in 3 subfamilies. Only family members of 
    rat and hamster are depicted.

2)  this msf file is put in the program "CLUSTALW"
3)  the tree made in this program is a .phb-file
4)  the phb-file is visualized in the program "TREEVIEW"

The problem is that one protein is not put in the right subfamily.

Does anyone know how I can make the most reliable phylogenetic tree ? Is my 
way of working really bad or gives it already a good impression ?

Thanks for your reply

Marc