> I would like to ask how do I read the tree? I could get the output
> printing during the multiple alignment. If I have N sequences, there
> are N-1 groups. Also, a .dnd file will be generated, I really do not
> know the meaning inside and how do I read this. Could anyone help?
These files are not realy human-readable, unless you only have a few
sequences (hint: try an alignment with only 3 or 4 sequences). Get
something like TreeView to convert this output into graphics.