Fu's and Tajima's using Arlequin

[avm]

Hi,

I am struggling with running neutrality tests using Arlequin. There is little to be found on the net unfortunately...

So I have 25 DNA sequences coding for a certain gene (9 alleles). I want to run Fu's and Tajima's on them.

I have opened my .fa file in Mesquite and exported as .phy. This file is then used to create the .arp input file for Arlequin. However, I am not sure of what settings I should choose. Data type should obviously be DNA, but genotypic data, known gametic phase and recessive data (I would guess genotypic data)?

Number of samples: Is that equal to the number of sequences I have?

In a step-by-step on how to run arlequin they say you should include haplotype list and genetic structure... I don't know how to make the haplotype list (I assume this means a list of the unique sequences). They refer to MacClade, but I'm working in a Mac and Mesquite doesn't seem to make haplotype lists...

Anyway, when I try and choose the tests I want to run (not incl haplotype list and genetic structure) under settings I can't choose the neutrality tests, it's greyed out! So what went wrong, must be something with the preparation of the .arp file...

Anyone who knows and would take some time and explain?
Would be very appreciated =)

Cheers,
Astrid

[arthurmelo]

Use DNASP software to estimate parameters of neutrality test. This software is more easy than arlequin.
If you want to use arlequin, I sugested that you create your input file using CREATE software.

And... sorry, but remmerber this community discuss methods and bioinformatics in NGS treatment.

[avm]

Thanks!
I managed. Ohh, well the analysis is on my NGS data