EZpcoa performs Principal Coordinates Analysis (PCoA) on aligned DNA sequences, with samples coloured by population.

A pairwise genetic distance matrix is computed from the alignment (K2P or p-distance) and classical multidimensional scaling (MDS) is applied. Ambiguous IUPAC characters are skipped per pair during distance computation.

Each unique haplotype is plotted as a pie chart at its mean ordination coordinates, with slices coloured by population and size proportional to the square root of haplotype frequency. Outputs include PC scatter plots, a scree plot, PC coordinate and eigenvalue tables, and the pairwise distance matrix.