Question: Population genetic inference from pooled-DNA microsatellite genotyping
2
gravatar for apaspati
8 months ago by
apaspati20
apaspati20 wrote:

Hello,

I have a dataset from genotyping pooled dna, which has the informacion of the allele frequencies for the microsatellite loci in each populations e.g.

3 populations

4 loci

number of alleles/loci 
2   3   2   2   4

pop L01.01  L01.02  L02.01  L02.02  L02.03  L03.01  L03.02  L04.01  L04.02  L05.01  L05.02  L05.03 
L05.04
pop01   0.02    0.00    0.14    0.00    0.78    0.51    0.49    0.90    0.10    0.00    0.00    1.00    0.00
pop02   0.00    0.00    0.00    0.00    0.49    0.45    0.55    0.93    0.07    0.22    0.47    0.31    0.00
pop03   0.00    0.00    0.00    0.00    0.52    0.27    0.73    0.72    0.28    0.20    0.59    0.21    0.00

I have been looking for an R package to perform basic population genetics statistics and calculate
genetic diversity, Fis and Fst, private alleles, pairwise genetic distances (e.g. Nei´s), null alleles, allelic richness but also I would like to test for isolation by distance.

However all the packages I find require datasets of individual allele frequencies.

Does anyone know any R package or programme that is adapted to population allele frequency datasets?

Thank you for your help!

Best regards! Angeliki

pooled dna microsatellites R • 248 views
ADD COMMENTlink modified 8 months ago by zx87546.5k • written 8 months ago by apaspati20
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