alllele number over loci equal to the number of individuals (arlsumstat)?

[Rosalía Piñeiro Portela]

I have simulated 10 microsatellites data with fastsimcoal2.

I need to calculate the mean nr of alleles over loci  (K_1) as summary statistic (with arlsumstat).

However, I  get  K_1 estimates equal to the number of samples in all simulated datasets.

I am going crazy trying to find where  the error is...

Any ideas?

Thank you very much in advance!

Best regards,

Rosalía

[Rosalía Piñeiro Portela]

It was the format of ark_run.ars file (not a mac vs pc problem). It is a shame that arlsumstat does not warn about this but it makes the wrong calculations anyway.

[Laurent Excoffier]

It is always good to use your ars file with the windows version of arlequin to be sure that it does what it is supposed to do.

But you should never tamper with ars files as is explicitly mentioned in the header of these files:

i.e.

             DO NOT EDIT THIS FILE BY HAND UNLESS YOU KNOW EXACTLY WHAT YOU

               ARE DOING. ERRONEOUS COMPUTATIONS MAY RESULT AS A CONSEQUENCE !!!

[gilber...@gmail.com]

Dear Laurent,

I am experiencing the same problem running ./LaunchArlSumStat.sh (K_1 summary statistic = sample size).

In my case I am producing the arl_run.ars file with Windows Arlequin. Then directly import it into a Unix server without any editing.

Cheers,

Mike

[Martin Stoffel]

I am having exactly the same issue!

[Rosalía Piñeiro Portela]

Dear Martin,

Have you managed to solve this issue of K_1 statistic equal to sample size? I haven't…

Best wishes,

Rosalía

[ddme...@gmail.com]

I am having the same problem. Does anyone have a solution?

[ddme...@gmail.com]

All right, I think I found the problem, which was - in my case - that I saved the data in haplotypic (i.e. the default) format instead of genotypic.
My theory is that when you save the data in haplotypic format (which is available for the simulated data), K_1, K_2, ..., mean_K will refer to the mean number of segregating haplotype alleles in the population instead of mean number of segregating SNP alleles (if you simulated SNP, as I did). Switch the output format to genotypic (use the "-g" or "--genotypic" option of fastsimcoal2) and you will have the mean number of SNP alleles (or whatever markers you simulated).
Note that the number of haplotype alleles can easily be as high as the number of simulated individuals (x2 in case of diploids).

I am not sure about this, but probably Mr. Excoffier or an other developer can confirm it.