rDNAbin: Random DNA Sequences

In ape: Analyses of Phylogenetics and Evolution

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)

ape documentation built on April 3, 2025, 7:53 p.m.