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Software For Amova And Population Comparison
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6.5 years ago
Portugal

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!

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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?

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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....

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

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I thought about that...

anyway thank you for you help

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20 months ago
Sabine • 60
India

could you please tel me which is the data input format ? thank you

i have some data need to be analysed by arlequin

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