[Bioperl-l] function for duplication events?

Mark A. Jensen maj at fortinbras.us
Thu Feb 19 23:56:33 EST 2009

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 
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.)
----- 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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