According to PowerMarker V3.0 manual, this software has been specifically designed to analyze SSR and SNP data. However, by literature review we find some publications on ISSR markers that used PowerMarker for data analysis. I would be grateful if you could kindly upload a sample input file of 0/1 data for this software.
I employed SRAP data (0/1 data) for the diversity and association analysis in Chinese fir, and a sample input file of 0/1 data for PowerMarker was provided in attachment.
Several steps are as follows:
1. input 0/1 data in Excel as the sample provied.
2. Open PowerMarker (the date of PC should be changed to the year 2012 or ago if needed to make sure the software work), and then copy the Excel data, and click PowerMarker dataset, choose “From clipboard", use "colume delimeters" “Comma"和"Space", and Next, click Sample, Categorical, and then Level-1 column “Sample”，Missing category input 1，and Next，Finish
3 .click Analysis what you needed.
Try it, and good luck.
Dear Dr. Zheng,
Thank you very much for your help and consideration.
In attached file there are two loci per marker (primer pair) and 19 independent samples while I have more than ten loci per marker and 36 populations containing 8 individuals. Thus, I should define my populations and markers for software. Moreover, in ‘Data Type’ option, only the ‘This dataset is haplotype data’ pathway allows us to go to the next step.
[I’m not sure about the pathway.]
“I have more than ten loci per marker and 36 populations containing 8 individuals.”?
You means that there have a large number of markers (e.g. more than 500 loci) for your populations?
If so, you are right, you should define your populations and markers for PowerMarker. And in fact, the transformation of‘0 to 0/0’ and‘1 to 1/1’could be achieved by Excel replacement step for a 0/1 matrix.
I am sorry for an error of ‘colume delimeters’ ‘Comma" and ‘Space’. ‘Comma’ should be changed to ‘Tab’. And there have no a step of selection of ‘This dataset is haplotype data’.
I hope my suggestions will help you.
Using four NBS primers and two restriction enzymes (totally 8 combinations) we got more than two loci per individual with each combination. Enclosed please find an example.
My matrix could not be 0/1 because I got more than two loci.
NBS-encoding gene family comprises many members, and it was comprehensive that the PCR amplification of this gene family using NBS primer combination sets would generate a series of NBS loci.
I think the result could be recorded as a binary matrix, with codon of 1 and 0 representing presence and absence of a band at a particular location (each locus) in each lane respectively. Therefore, some genetic parameter such as PIC and Nei’s gene diversity could be calculated by PowerMarker.
I hope my suggestions will help you.
help me out my powermarker not working dont know how to anlyze the table once added in powermarker
Dear Kiran
You can change the year from your computer setting to 2007 the program will be working.
Ali Pourkhaloee
Good day to you
I'm facing the same problem and read the comments which are really enlightening, but unfortunately, I'm still facing the problem with the input file of POWERMARKER for ISSR markers, would please provide an example of the input file , I'll be grateful , Thank you
I am getting 2-6 alleles for SSR data on mustard. May I request anybody to kindly share the input file of SSR allelic data for powermarker analysis
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