number of sequences to return. If NULL (default), all
sequences are returned.
model
a character string specifying the evolutionary model to be used.
See dist.dna for more information.
pairwise.deletion
a logical indicating whether to delete sites
with missing data. See dist.dna for more information.
as.haplotypes
treat sequences as haplotypes (TRUE) or expand
haplotypes to one sequence per individual (FALSE). If the latter,
individual frequencies are used in cluster formation.
simplify
if there is a single locus, return result in a simplified
form? If FALSE a list will be returned wth one element per locus.