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Old 08-23-2016, 11:56 PM   #1
vivi7
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Location: Aarhus, Denmark

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Default Understanding Pi estimates

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 at 12:08 AM. Reason: Wrong spelling
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