[Bioperl-l] clustering trees obtained from phylip neighbor

Roy Chaudhuri roy.chaudhuri at gmail.com
Wed Mar 2 13:06:48 EST 2011


Hi Moitrayee,

I know a fair amount about phylogenetics, but I have no idea what you 
mean by the "fork level" of a tree. Perhaps you could use your example 
tree to explain what input you want the user to specify, and what output 
you want to produce?

Roy.

On 01/03/2011 11:22, moitrayee at mbu.iisc.ernet.in wrote:
> Dear BioPerl Users/Developers,
>
> I have obtained a tree using a very large number of nodes
> (1000 nodes) using the neighbor joining in PHYLIP. A small
> test output looks like the following:
>
>    +------------------------------------------------Bovine
> --6
>    !    +-------------------------------------------Mouse
>    +----5
>         !                        +------------------Gibbon
>         +------------------------4
>                                  !    +-------------Orang
>                                  +----3
>                                       !   +---------Gorilla
>                                       +---2
>                                           ! +-------Chimp
>                                           +-1
>                                             +-------Human
>
> The outtree in Newick format is:
>
> (Bovine:0.81551,(Mouse:0.73556,(Gibbon:0.31044,(Orang:0.24003,
> (Gorilla:0.16418,(Chimp:0.13460,Human:0.13460):0.02958):0.07586):0.07040):0.42512):0.07995);
>
>
> I am trying to obtain the cluster at different fork level of this tree.
>
> The fork level goes as an user input. I looked into the link
>
> http://www.bioperl.org/wiki/HOWTO:Trees#Related_Modules
>
> But the Node connectivity methods described there does not apply
> to the tree I have pasted above.
>
> Any help / suggestions would be thankfully appreciated.
>
> Thanks a lot in advance and looking forward to hear from you.
>
> Sincere Regards,
> Moitrayee Bhattacharyya
> Molecular Biophysics Unit,
> Indian Institute of Science
> Bangalore-560012
> India
>
>
>



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