Hi, I have a dnd file in the format like ((A:0.33139,B:0.29208):0.04409,(C:0.28550,D:0.28440):0.03647,(E:0.35068,F:0.38974):0.03419); I want to find which left parentthesis matches which right parenthesis. Of course, in the example I listed, it is simple to figure out, but it would be very complex when I get thousands of nodes. Can Bio-Phylo module help on this? Or what Bioperl module I should use to get this problem solved. Thanks a lot! Tony