How to read the dendrogram tree in CLUSTAL W?
Gys de Jongh
Gys_nospam_deJongh at planet.nl
Thu Aug 7 09:25:23 EST 2003
"ABC" <cdcer at hongkong.com> wrote in message
news:d618a781.0308040042.c7f0058 at posting.google.com...
> 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?
> 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?)?
> And for the printing, how the sequences are joined together in the
> 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"?
goto : http://web.hku.hk/~xxia/
copy the above .dnd file to the clipboard
then do : phylogenetics => paste tree into tree display panel
You will see the cluster tree
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