[Bioperl-l] function for duplication events?

[Jason Stajich]

If you mean infer duplication vs speciation events via a tree I would  
suggest taking at look at these tools. RIO, njtree/treebest,  
softparsemap, or Notung.
   http://rio.janelia.org/
  http://treesoft.sourceforge.net/treebest.shtml
  http://www.cbu.uib.no/~steffpar/softparsmap/
  http://www.cs.cmu.edu/~durand/Notung/

Probably njtree/treebest is the easiest to get started with.

We talk about some of these a little in our tutorial from '07 and from  
the '06 hackathon.
http://jason.open-bio.org/Bioperl_Tutorials/ISMB2007/
  https://www.nescent.org/wg_phyloinformatics/Reconcile_Trees_Documentation 
.

Also see Dannie Durand et al review
  http://dx.doi.org/10.1016/j.tig.2006.01.002

-jason
On Feb 19, 2009, at 12:37 AM, Chrysanthi A. wrote:

> Hi,
>
> I was wondering if there is a method in order to visualize a tree by  
> parsing
> a nexus format and also, I would like to identify the duplication  
> events.
> Are there any functions that will give me the duplication events?
>
> thanks a lot,
>
> Chrysanthi
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Jason Stajich
jason at bioperl.org