Intrapop neutrality tests
(based on the Frequency Spectrum)

The method in brief

Through this webpage, you will compute few standard neutrality tests that are solely based on the frequency spectrum: More tests can be implemented if requested.
For now, sites with indel are completely ignored and when more than 2 symbols exist at a site, the second most frequent is used to compute the frequency. All the other ones are pooled and considered as the most frequent one.

Online version of the neutrality tests

Please copy/paste your sample (aligned fasta format)

Please copy/paste your outgroup (aligned fasta format)

Select your tests
D (Tajima 1989) D2 / D*2 (Fu and Li 1993) F / F* (Fu and Li 1993)
H (Fay and Wu 2000) E (Zeng et al. 2006) Y / Y* (Achaz 2008)
Ω / Ω* (Achaz, 2009)

Choose if the statistics are normalized by their standard deviations:
Yes, do normalize
No, do not normalize

If you want to use the Ω tests, copy/paste your two ω vectors (or ω* if no outgroup is given) (Please refer to Achaz, 2009 for Ω tests).
Each value of the weight vector (any set of positive value) is separated by ONE blank character. Let n be the sample size (outgoup excluded). If an outgoup is given, the number of value in each vector should be equal to (n-1). If no outgoup is specified, the vector size should be equal to floor(n/2)


This program has been written in C. It is originally part of a library (libdiversity) of functions that does manage aligned sequences and compute many standard population genetics metrics (The library is available upon request). The source of this stand-alone web-adapted version can be viewed at neutralitytst.c (compiled as 'gcc -o neutralitytest.cgi -O2 -DMACOSX neutralitytest.c -lm'). I would be happy to incorporate any interesting suggestions.


If you have any suggestions/comments, please send them to Guillaume Achaz:

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