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?)?
>
> (
> (
> (
> A:0.03469,
> B:0.13391)
> :0.03656,
> C:0.04385)
> :0.00984,
> (
> (
> (
> D:0.01353,
> E:0.05098)
> :0.47204,
> F:0.22940)
> :0.06574,
> (
> G:0.08382,
> H:0.04118)
> :0.04137)
> :0.05021,
> (
> (
> I:0.05217,
> J:0.01759)
> :0.01211,
> K:0.07481)
> :0.01770);
>
>
>
>
> And for the printing, how the sequences are joined together in the
> tree?
>
> There are 10 groups
> Aligning...
> 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"?


Hi,
goto : http://web.hku.hk/~xxia/
download DAMBE
copy the above .dnd file to the clipboard
then do : phylogenetics => paste tree into tree display panel
You will see the cluster tree
hth

 --
Gys






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