[Bioperl-l] [Fwd: Re: Modules in Bio:Tree]

[Sudeep Mehrotra]

Hello Jason,
Your suggestion worked. Thanks.

I have two format (NEXUS and NEWICK) for the same tree. I want to obtain 
a "clade list" in other words is there a way to obtain the leaves which 
are members of a clade.
For example,part of NEXUS file has following entry:
         
       other entries
          .......
        655 Deinococcus_geothermalis,
        656 Deinococcus_radiodurans,
        657 Thermus_thermophilus,
        658 Thermus_sp.
;
other entries........
(((((655,656)[])[])[],(((657,658)[])[])[])[])[])[])[]);

 From the tree I can observe that 657 and 658 are members of a subclade 
and 655 and 656 are member of another subclade and both these belong to 
one clade.
I want to get this membership information. I tried looking for a module 
in Bio::Tree but not able to find any.

In Bio::NEXUS package there is a module "walk" which I thought would 
work for me, but it does not. Also, the Bio::NEXUS package is just not 
working for me. From the documentation the input file they are using it 
different from what I have.

Is there any way I get the membership information as shown earlier.

Cheers

-- 
Sudeep Mehrotra (Ph.D. Candidate)
McGill University and Genome Quebec Innovation Center

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