Please advise me on how to use the GenAlex software?

To prepare data from an ISSR (Inter Simple Sequence Repeat) marker gel for analysis with the GenAlex program, you will need to follow these steps:

Scan the gel and save the image: Use a gel scanner or a digital camera to capture an image of the gel. Save the image in a format that can be read by the GenAlex program, such as TIFF or JPEG.

Extract the data from the image: Use the GenAlex program to extract the data from the image of the gel. This may involve adjusting the contrast and brightness of the image and setting the threshold values to separate the bands from the background.

Assign the bands to the appropriate samples: Identify the bands on the gel that correspond to each sample, and assign them to the appropriate sample in the GenAlex program.

Analyze the data: Use the GenAlex program to perform statistical analyses on the data, such as determining the number and percentage of polymorphic loci, the average and effective number of alleles, heterozygosity, and the Shannon information index.

To determine the number and percentage of polymorphic loci, you can use the GenAlex program to count the number of bands that are present in more than one sample and divide this by the total number of bands. The percentage of polymorphic loci can then be calculated by multiplying this value by 100.

To determine the average and effective number of alleles, you can use the GenAlex program to calculate the number of alleles at each locus and the frequency of each allele. The average number of alleles can then be calculated by summing the number of alleles at each locus and dividing by the total number of loci. The effective number of alleles can be calculated using the Shannon information index, which takes into account the frequency of each allele at each locus.

To determine heterozygosity, you can use the GenAlex program to calculate the proportion of loci that are heterozygous, or have two different alleles. This can be done by dividing the number of heterozygous loci by the total number of loci.

To determine the Shannon information index, you can use the GenAlex program to calculate the frequency of each allele at each locus and use this information to compute the Shannon index, which is a measure of the diversity of the alleles within the population.

Per Kryger

These are some of the basic calculations given by GenAlEx. Follow the tutorials that are on the same webpage as GenAlEx, and voila, you will find all the information there. GenAlEx deserves praise, for having both a set of tutorial and a little manual, it is very user friendly. Good luck!

Peter Hristov

Dear Per,

I can help you. Just send me your data on email: [email protected].

Best,

Peter

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