Calculate AMOVA & MDS

Please perform online AMOVA as follows

  1. Use your population sample(s) file (Excel) to start AMOVA. Be sure to provide haplotypes only for markers you are going to use in your AMOVA calculation. E.g. when using a PowerPlex Y23 file, all AMOVA calculations are based on full Y23 haplotypes.
  2. Select populations and/or whole national databases from the YHRD. You can select up to 10,000 haplotypes in sum.
  3. Check and adjust the calculation options/preferences as needed.

The result will consist of: a table of calculated pairwise FST or RST and p-values (as .csv file), a MDS plot (as .pdf file) and additionally, if "relaxing" was selected, a relaxation file with all the clusters built prior calculation (as .txt file).

Constraints / modifications applied to the set of haplotypes:

  • All haplotypes with empty or otherwise unspecified alleles (according to the markers given in the table header) will be removed.
  • All haplotypes with alleles which do not comply with the markers nomenclature (e.g. ">24" or "OL") will be removed.
  • All haplotypes with intermediate alleles (e.g. "14.2") will be removed.
  • All haplotypes with null-alleles will be removed.
  • All haplotypes with duplicated alleles (except DYS385 and DYF387S1) will be removed.
  • All haplotypes with triplicated (or even more) alleles will be removed.
  • DYS389I will be substracted from DYS389II.

If you don't know what AMOVA or MDS is, read our summary.

If you don't know how to export your samples using Applied Biosystems® GeneMapper® ID/ID-X please read our instructions.

If you don't know how to set up an Excel-, OpenOffice- or CSV-spreadsheet to store your population data, please see our example or read our instructions.

In either case, please consider checking your file before you are going to use it here.

For more information on AMOVA (Analysis of Molecular Variance) please see Excoffier L., Smouse PE., Quattro JM. (1992), 'Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.', Genetics 131(2), 479-91 [Pubmed]

For more information on the MDS calculation please see Kruskal , J. B. (1964), 'Nonmetric Multidimensional Scaling: A Numerical Method', Psychometrika 29(2), 115-129

* See FAQ/Glossary ( for further explanations of abbreviated terms used here