> For example, if a have a .dnd as follows, what is the meaning? How do
> I divide them into different groups and realize them into different
> groups? (Also, what are the meaning for the number next to the
> labels?) Do '(' mean something (represent the branch in the tree?)?
This is a compressed format... It's hard to read it without a software such
as Phylip or ARB... Anyway each branch represents a group in the tree and
the numbers are the distances of the nodes.
> There are 10 groups
> Group 1: Sequences: 2 Score:3497
> Group 2: Sequences: 3 Score:1726
> Group 3: Sequences: 2 Score:3674
> Group 4: Sequences: 3 Score:3551
> Group 5: Sequences: 6 Score:2905
> Group 6: Sequences: 2 Score:1867
> Group 7: Sequences: 8 Score:2008
> Group 8: Sequences: 9 Score:2551
> Group 9: Sequences: 2 Score:5835
> Group 10: Sequences: 11 Score:1517
> Alignment Score 25915
>> What are the meaning of the "Score:" and "Alignment Score"?
In order to understand these scores you should know how ClustalW works.
Roughly "Score" means how much two sequences are related into a group (the
score is given to the pairwise alignment of two sequences into a group or
to the alignment of a sequence with a group)... the higher the better.
The "alignment score" is a score given to the entire alignment. These scores
don't have an absolute importance because they depend on the parameters you
use to generate the alignment (gap scores, matrices...). You can modify
these parameters and see how scores change, a good multi-alignment implies
scores not changing widely.
Consider that there's no optimal algorithm to align sequences and to build