xAMOVA is a program that extends the AMOVA (analysis of molecular variance, Excoffier et al 1992) to crossed designs where there are two factors (i.e. a two-way AMOVA). Components of variance are estimated for each factor, and simulation-based significance tests are performed for each factor individually and the model as a whole.

To download xAMOVA click here. The zip file contains

Information on how to format your data for use with xAMOVA, running the program, and example analyses are contained in the file README.txt. A publication for the methodology in xAMOVA is being prepared with collaborators in France and Japan. In the meantime there are details in Chapter 3 of my thesis. The original AMOVA reference is

Excoffier, L., P. E. Smouse and J. M. Quattro (1992)
Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
Genetics 131: 479-491. (pdf)

Example screen shot: