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Lauro

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gabranch
Jan 18^th, 2010 at 2:46pm

I have a question. I am working with a set of vesicular stomatitis sequences, I performed SLAC , IFEL, FEL and I did not find a signal of positive selection only negative, however when I tried with Gabranch I got some branches with dn/ds more than 1.00. How must I interpret this results? As a positive selection only at population level?

Thank you for your Help,

Lauro.

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Sergei

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Re: gabranch
Reply #1 - Jan 19^th, 2010 at 12:39pm

Hi Lauro,

SLAC/IFEL/FEL test for selection at a site averaging over all branches. Hence, if you have positive selection only on a few lineages in a big tree, the signal will be diluted by the other branches. GABranch tests for selection at a branch, averaging over all sites. Your finding simply suggests that the sequence in your sample have undergone episodic diversifying selection along some lineages.

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Sergei

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Lauro

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Re: gabranch
Reply #2 - Jan 19^th, 2010 at 2:39pm

Thank you Sergei for your comments.
I am analyzing a set of sequences of VSV from different parts of Mexico, typically is say that VSV evolves over positive selective pressure but I am finding that negative is maybe more important. Other authors have used this site to calculate dN/d/S (SNAP/README) based on Nei and Gojobori (1986) method and they have find high values of positive selection. If I analyze my data in that web server I get the same. Could you tell me some differences between the use of this method and your methods.

2.- Based on the results by your methods could I conclude that negative selection plays a more important roll that positive. (my sample size is 138 from 5 years)

Thank you
Sincerely,
Lauro.

Sergei wrote on Jan 19^th, 2010 at 12:39pm:

Hi Lauro,

SLAC/IFEL/FEL test for selection at a site averaging over all branches. Hence, if you have positive selection only on a few lineages in a big tree, the signal will be diluted by the other branches. GABranch tests for selection at a branch, averaging over all sites. Your finding simply suggests that the sequence in your sample have undergone episodic diversifying selection along some lineages.

Best,
Sergei

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