How to read the dendrogram tree in CLUSTAL W?

ABC cdcer at hongkong.com
Tue Aug 5 11:27:38 EST 2003


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"?

Thank you very much!!!
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