Description Usage Arguments Details Value Author(s) See Also Examples

`base.freq`

computes the frequencies (absolute or relative) of
the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
sample of sequences.

`GC.content`

computes the proportion of G+C (using the previous
function). All missing or unknown sites are ignored.

`Ftab`

computes the contingency table with the absolute
frequencies of the DNA bases from a pair of sequences.

1 2 3 |

`x` |
a vector, a matrix, or a list which contains the DNA sequences. |

`y` |
a vector with a single DNA sequence. |

`freq` |
a logical specifying whether to return the proportions (the default) or the absolute frequencies (counts). |

`all` |
a logical; by default only the counts of A, C, G, and T are
returned. If |

The base frequencies are computed over all sequences in the sample.

For `Ftab`

, if the argument `y`

is given then both `x`

and `y`

are coerced as vectors and must be of equal length. If
`y`

is not given, `x`

must be a matrix or a list and only
the two first sequences are used.

A numeric vector with names `c("a", "c", "g", "t")`

(and possibly
`"r", "m", ...`

, a single numeric value, or a four by four matrix
with similar dimnames.

Emmanuel Paradis

`seg.sites`

, `nuc.div`

(in pegas), `DNAbin`

1 2 3 4 5 6 7 8 |

```
a c g t
0.3065414 0.2613083 0.1260264 0.3061239
a c g t
4405 3755 1811 4399
a c g t r m w s k y v h d b n -
4405 3755 1811 4399 0 0 0 0 0 0 0 0 0 0 105 0
?
0
[1] 0.3873347
a c g t
a 287 0 2 0
c 0 247 0 5
g 5 0 119 0
t 0 4 0 290
a c g t
a 287 0 2 0
c 0 247 0 5
g 5 0 119 0
t 0 4 0 290
a c g t
a 292 1 1 0
c 0 246 0 3
g 1 0 120 1
t 0 10 0 283
```

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