I would like to calculate and compare allelic richness (or similar parameters) of 10 populations with different sample sizes. I thought to use a rarefaction method, in order to adjust the estmates for the different sample sizes. My dataset deals with codominant markers (6 microsat loci with more than 20 alleles/locus). Can anyone indicate a program for this purpose? Thanks.
Dear Ferruccio:
You can use FSTAT for that purpose.
Best regards
José Gabriel
Hi Ferrucio
There is also HP rare which should do rarefaction (but yes FSTAT is good for testing)
http://www.montana.edu/kalinowski/Software/HPRare.htm
best
Didier
Yes you can use FSTAT but there is this very simple program called GenALEx that allows you to calculate other parameters including number of alleles and population differentiation which can give you an additional picture of how these variation in allelic richness is reflected when you compare your populations.
I beileve FSTAT is better to account for differences in population sizes using SSRs.
Do you have null alleles in your dataset? If not you can also try StandArich, it's an R package.It gives you standardized allelic richness but also some cool graphics with allelic frequency per population.
Actually FSTAT does rerefaction! I had not realize it, despite I've been using FSTAT since its earliest versions.... Thank everybody for advices!
You can also do it in R using the PopGenReport package. To get the full effect, you need a LaTeX editor installed, but you can run the allel.rich function without it.
One very effective package that has not been mentioned is 'Heirfstat' in R.
The function allelic.richness calculates the rarefied allelic count. In my view, it is easier to use that FSTAT and is faster than GENALEX.
http://cran.r-project.org/web/packages/hierfstat/index.html
Adze also works well and can handle batch processing of multiple files:
https://web.stanford.edu/group/rosenberglab/adze.html
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