How to read the dendrogram tree in CLUSTAL W?

joe at removethispart.gs.washington.edu joe at removethispart.gs.washington.edu
Tue Aug 5 17:22:47 EST 2003

In article <d618a781.0308040042.c7f0058 at posting.google.com>,
ABC <cdcer at hongkong.com> wrote:
>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 so on)

As this is the Newick tree file format, and as I was the convener of the
committee that standardized it, I guess I should be the one who answers.
The parentheses indicate nestings and the numbers indicate "branch lengths".
For a clear description see the Newick tree format web page at our site:

Joe Felsenstein         joe at removethispart.gs.washington.edu
 Department of Genome Sciences, University of Washington,
 Box 357730, Seattle, WA 98195-7730 USA

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