Understanding Pi estimates

vivi7

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Join Date: Mar 2014

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Understanding Pi estimates

08-23-2016, 11:56 PM

Hi all,

We are using MEGA7 to estimate genetic diversity values from RAD seq data. Does any of you knows what is the difference between the Pi estimated with the option "Distance -> Compute Mean Distance" and the ones estimated with "Selection -> Tajima's test of neutrality"?

In the manual the definitions are the same but the two tests give very different results for the same dataset:
- Distance matrix: p-distance - It is obtained by dividing the number of nucleotide differences by the total number of nucleotides compared.
- Tajima's test of neutrality: nucleotide diversity is defined as the average number of nucleotide differences per site between two sequences.

Thanks in advance
Vivi

Last edited by vivi7; 08-24-2016, 12:08 AM. Reason: Wrong spelling
Tags: genetic diversity, mega

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