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To measure the apportionment of variance between pairs of populations, a method called AMOVA (Analysis of Molecular Variance) can be used (?). In case of Y-chromosome profiles it considers the variance in the number of STR repeat units at DYS loci within and between populations. This method takes into account the molecular relationship of alleles, rather than just their frequency. The AMOVA method can be applied to measure the genetic distance between your population sample and reference samples from the YHRD.

By using the online AMOVA program it is possible to calculate Φ_st (apportionment of within/among population variance) between pairs of populations. To test for significance p-values will be calculated as well (10,000 permutations). Please perform online AMOVA as follows:

1. Upload a population sample from your files. This file should contain one haplotype per row and a header naming the columns. Only Microsoft Excel file will be accepted (example XLS sheet).
2. check the file for correctness of locus names and alleles (please note that duplicated and intermediate alleles well be omitted from the calculation)
3. check the mapping of columns from your file to database columns
4. select from YHRD up to 9 population samples for AMOVA comparison

The result will include:

1. Calculated pairwise Φ_ST and p-values as CSV file
2. MDS as PDF file. The MDS calculation is based on Kruskal's non-metric MDS algorithm.

Calculate your AMOVA now Please note: the larger the sample sizes, the longer it needs to complete the calculation.