This function prints on the console a series of diagnostics on the
set a aligned DNA sequences. If alignment gaps are present, their
width distribution is analysed, as well as the width of contiguous
base segments. The pattern of nucleotide diversity on each site is
also analysed, and a relevant table is printed.
If plot = TRUE
, four plots are done: an image of the
alignement, the distribution of gap widths (if present), the Shannon
index of nucleotide diversity along the sequence, and the number of
observed bases along the sequence.
If the sequences contain many gaps, it might be better to set
check.gaps = FALSE
to skip the analysis of contiguous
segments.