[Bioperl-l] clustering trees obtained from phylip neighbor

moitrayee at mbu.iisc.ernet.in moitrayee at mbu.iisc.ernet.in
Tue Mar 1 06:22:54 EST 2011


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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