"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
