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:

• D (Tajima, 1989)
• D₂*, F*, D₂, F (Fu and Li, 1993)
• H (Fay and Wu, 2000)
• Y and Y* (Achaz, 2008)
• Ω tests --Generic tests (Achaz, 2009)--

More tests can be implemented if requested.

Online version of the neutrality tests

Please copy/paste your sample (aligned fasta format)
>seq_1 GCGAAT-GC >seq_2 AGGTATTGC >seq_3 GCGTATTTT >seq_4 GCGTATTTT >seq_5 GCGTATTGC >seq_6 GCGTATTGT

Please copy/paste your outgroup (aligned fasta format)
>seq_o GGGTATTGT

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)
ω₁
ω₂

Sources

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.

Contacts

If you have any suggestions/comments, please send them to Guillaume Achaz: achaz@abi.snv.jussieu.fr