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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Theoretical questions >> Sequence Analysis >> AIC-c as a measure of recombination rate? http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1306070040 Message started by michiel on May 22^nd, 2011 at 6:14am

Title: AIC-c as a measure of recombination rate?
Post by michiel on May 22^nd, 2011 at 6:14am

Dear fellow datamonkeys,

I am looking for a method that quantifies recombination rate in my many single gene alignments (I am not interested in specific breakpoints etc). Could I plot the AIC-c score as a proxy for recombination rate?

Many thanks for any suggestions you might have!

Best Wishes, Michiel

Title: Re: AIC-c as a measure of recombination rate?
Post by Sergei on May 23^rd, 2011 at 10:48am

Hi Michiel,

Unfortunately, AIC-c would not be useful as a quantifiable measure of recombination rate because it conflates the size of the recombination effect (rate) with evolutionary change (divergence) -- and some other effects as well.

Sergei

Title: Re: AIC-c as a measure of recombination rate?
Post by michiel on May 23^rd, 2011 at 12:40pm

Dear Sergei,

thank you for your rapid reply. I suspected an effect of divergence (more polymorphisms > more power to detect recombination). However, since I have a large datset, perhaps I could statistically correct for this effect (e.g. using an ANCOVA)? Or is there something I am overlooking?

Best Wishes, Michiel