Dear Sara Malito,

Please find the attached file, containing the manual for powermarker. I hope it will help you. In addition, I can help you to set the dataset on GeneMarker Software. Good Luck

Hi Ali, I had a paper accepted with major revisions and they asked me the following analysis on SSR data: MAF (Major Allele Frequency), PIC (Polymorphic information content), Probability of identity (PI) e FN (estimated null Allele Frequency). I read several paper and it seems that powermarker do all these parameters. Does GeneMarker do the same?

For these analysis, I would like to suggest you POPGENE software. All these can be done with one click. Please find the attached file. It's easy to use. let me know, if you need more help. Than you

Hi Ali, thanks a lot for your quick answer. I used Popgene, but unfortunally I did not find the parameters that the reviewer ask me. Should it be something that I could obtain from the principal calculated by POPGENE?

My pleasure. MAF (Major Allele Frequency) might be similar as Allele Frequency in popgene. For the Probability of identity (PI) we could use Homogeneity test in popgene. However for the PIC Value, actually i did it manually in Excel sheet. For Null allele frequency: A simple approach (although clearly of limited utility) was to estimate a null allele frequency (p) as the square root of the frequency of individuals whose DNA at the focal microsatellite locus failed to amplify (ie, presumed homozygotes for the null allele). Another intuitive method was to base p on a count of the number of null alleles as inferred from parentage analyses when (as mentioned above) a known parent and its offspring show different ‘homozygous’ genotypes at the focal locus only. Assuming that the null allele in a sample of N diploid individuals is rather rare, its frequency can then be estimated as the number of inferred null heterozygotes divided by 2N.

PowerMarker generally works on our computer by changing our date of computer before 2011 and sometime it used to crash. So, If you have any problem using it. You can also try GenAlEx 6.5.. which is just and extension to MS excel and do the same thing in MS excel ....

GenAlEx 6.5 for Probability of identity (PI) and Cervus to analysis PIC (Polymorphic information content)

Dear Sara,

Analysis using Power Marker requires genotypic data set similar to the data set that is used for co-dominant marker analysis using Popgene.

Hope this will help you in solving your problem.

Powermarker runs in system provided the date of system (PC/laptop) is set before 2015. Follow and Enjoy the analysis.