[Bioperl-l] function for duplication events?

Chris Fields cjfields at illinois.edu
Fri Feb 20 00:28:03 EST 2009

There is also clustering using various algorithms such as MCL.  I have  
used it for a project here, and Jason has directly donated code to the  
cause.  See here:


Note this requires an all-v-all BLASTP run prior to the clustering.


On Feb 19, 2009, at 10:56 PM, Mark A. Jensen wrote:

> Chrysanthi-
> I believe the positive identification of duplicated genes is tricky-  
> The question is, do you a have a list of known paralogous gene pairs,
> or do you need to sift the sequence for likely candidates. I think  
> it should be "relatively straightforward" (haha!) to look down trees  
> for the most recent common ancestor of known pairs, and use that node
> as an approximation for the duplication event.
> If you don't know what genes you have are duplicates of each other,
> then you might have a look at the algorithm in http://www.ncbi.nlm.nih.gov/pubmed/12836682
> by Wen-Hsiung Li, Zhenglong Gu, et al. This paper is relatively
> old (2003)--it's not my specialty; I'm sure many developments have  
> ensued since. Gu has done nice computational work in this area and  
> you might want to track him down. (If you want this paper and can't  
> access it, contact me off-list.)
> Mark
> ----- Original Message ----- From: "Chrysanthi A."  
> <chrysain at gmail.com>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Thursday, February 19, 2009 3:37 AM
> Subject: [Bioperl-l] function for duplication events?
>> 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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