a matrix, a data frame, or a list which contains the DNA
sequences.
variance
a logical indicating whether to compute the variance
of the estimated nucleotide diversity.
pairwise.deletion
a logical indicating whether to delete the
sites with missing data in a pairwise way. The default is to delete
the sites with at least one missing data for all sequences.
Value
A numeric vector with one or two values (if variance = TRUE).
Details
The nucleotide diversity is the sum of the number of differences
between pairs of sequences divided by the number of comparisons
(i.e. n(n - 1)/2, where n is the number of sequences).
The variance of the estimated diversity uses formula (10.9) from Nei
(1987). This applies only if all sequences are of the same lengths,
and cannot be used if pairwise.deletion = TRUE. A bootstrap
estimate may be in order if you insist on using the latter option.
References
Nei, M. (1987) Molecular evolutionary genetics. New York:
Columbia University Press.