Software For Amova And Population Comparison

Question

[reis.a.rita]

Hello

I'm new with population genetics and I have allelic frequency data for 50 loci in 9 different populations and I need to compare the data between those populations but I don´t know any software to do that. I tried Arlequin but it only lets me input data for one locus at a time and I need all 50 loci at once.

If someone could help me with that I will be very grateful!

[David W]

Arlequin can use multiple loci, as can the the amova function in the R library ape: what exactly does your data look like, and what' the problem with getting it into arlequin?

[reis.a.rita]

I have frequency data from each allele per locus (50 biallelic loci) and I need to compare all loci at once and not locus per locus. Arlequin manual says single-locus treatment only, for allele frequency data so I have to create one project for each locus right?

Example of my data:

locus 1 
                      Pop 1  Pop2   Pop3  Pop 4  Pop 5 Pop 6 Pop 7  Pop 8 Pop9

Allele1 *    .7108  .6689  .5556  .5986  .3938  .7230  .4380  .5079  .5580 
Allele2 *    .2892  .3311  .4444  .4014  .6062  .2770  .5630  .4921  .4420

locus 2

Allele1*    .5904  .5722  .4537  .4648  .4938  .6520  .4310  .3253  .5020
Allele2*    .4096  .4278  .5463  .5352  .5062  .3480  .5690  .6747  .4970

And so....

[David W]

You need per-indivudal genotypes to do AMOVA, as it needs to estimate within-population variance. The aggergated frequencies don't give us that.

[reis.a.rita]

I thought about that...

Anyway thank you for you help

Answer 1

[Sabine]

Could you please tel me which is the data input format ? Thank you

I have some data need to be analysed by arlequin