Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

I'm reading Yang's computational molecular evolution and in the very first chapter it says the P distance is a "simplistic distance measure" between two sequences. It is the number of different sites / the total number of sites.

However, because back mutation and multiple hits cause inaccuracy it become weak over longer distances (large number of generations to most recent common ancestor, MRCA, I guess).

"The raw proportion p is usable only for highly similar sequences, with p <0.05 (5%, approximately)."

How far back in divergence time do we have to go for this p<5% to be violated? I assume it has to do with the mutation rate right? I'm trying to get a sense of scale on this for myself. Are we talking a distance of just a few generations (within species), the distance between two closely related species, or an even greater distance?

share|improve this question
    
Yes, obviously it depends on the mutation rate, which in turn depends on the locus you are dealing with and is organism-specific. –  har-wradim Feb 13 at 23:55

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Browse other questions tagged or ask your own question.