R: Random DNA Sequences

rDNAbin {ape} | R Documentation

## Random DNA Sequences

### Description

This function generates random sets of DNA sequences.

### Usage

    rDNAbin(n, nrow, ncol, base.freq = rep(0.25, 4), prefix = "Ind_")

### Arguments

`n` | a vector of integers giving the lengths of the sequences. Can be missing in which case `nrow` and `ncol` must be given.
`nrow, ncol` | two single integer values giving the number of sequences and the number of sites, respectively (ignored if `n` is given).
`base.freq` | the base frequencies.
`prefix` | the prefix used to give labels to the sequences; by default these are Ind_1, ... Ind_n (or Ind_nrow).

### Details

If `n` is used, this function generates a list with sequence lengths given by the values in `n`. If `n` is missing, a matrix is generated.

The purpose of this function is to generate a set of sequences of a specific size. To simulate sequences on a phylogenetic tree, see `simSeq` in phangorn (very efficient), and the package phylosim (more for pedagogy).

### Value

an object of class `"DNAbin"`.

### Note

It is not recommended to use this function to generate objects larger than two billion bases (2 Gb).

### Author(s)

Emmanuel Paradis

### See Also

`DNAbin`

### Examples

    rDNAbin(1:10)
    rDNAbin(rep(10, 10))
    rDNAbin(nrow = 10, ncol = 10)

[Package ape version 5.6 Index]