I've a set of nucleotide sequences and I used clustalw v.2.1 to align those sequences. The next thing I did was to generate a tree using the .dnd file in a Tree visualization software. I incorporated a -BOOTSTRAP function in the clustalw but the tree did not display the bootstrap value. I even checked the .dnd file with only listed the distance value but not the bootstrap value.
The command I used in the perl script for clustalw alignment was
system("$clustalw -INFILE=$in_file -OUTFILE=$out_file -TYPE=DNA -CLUSTERING=NJ -BOOTSTRAP=1000 -CONVERT=Phylip");
How can I display the bootstrap values in the tree? Is anything missing in my command? I did not get a clear explanation on it in the clustaw help file!!