This function computes the nucleotide diversity from a sample of DNA sequences or a set of haplotypes.

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`x` |
a matrix 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. |

`...` |
further arguments to be passed. |

This is a generic function with methods for classes `"DNAbin"`

and `"haplotype"`

. The first method uses 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 second method uses haplotype frequencies. It could be
that both methods give (slightly) different results because of missing
or ambiguous nucleotides: this is generally solved by setting
`pairwise.deletion = TRUE`

.

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.

A numeric vector with one or two values if `variance = TRUE`

.

Emmanuel Paradis

Nei, M. (1987) *Molecular evolutionary genetics*. New York:
Columbia University Press.

`base.freq`

, `GC.content`

,
`theta.s`

, `seg.sites`

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