Hi, and welcome!
Take a look at the pegas package which has an
amova function (yes, with an m), which returns
a list with a table of sums of square deviations (SSD), mean square deviations (MSD), and the number of degrees of freedom, and a vector of variance components.
I'm not in your field, but recommend looking at this because the package describes itself
Description Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum span- ning tree and network, and median-joining networks.
There's also an
MMD, mismatch distribution function that
draws a histogram of the frequencies of pairwise distances from a set of DNA sequences.