phyclust (version 0.1-34)

seqgen: Seq-Gen

Description

This function modifies the original standalone code of seq-gen developed by Rambaut, A. and Grassly, N.C. (1997).

Usage

seqgen(opts = NULL, rooted.tree = NULL, newick.tree = NULL, input = NULL,
       temp.file = NULL)

Value

This function returns a vector, and each element stores one line of STDOUT of seq-gen separated by newline. The vector stores in a class

seqgen. The details of output format can found on the website

http://tree.bio.ed.ac.uk/software/seqgen/ and its manual.

Arguments

opts

options as the standalone version.

rooted.tree

a rooted tree which sequences are generated according to.

newick.tree

a NEWICK tree which sequences are generated according to.

input

optional inputs of seq-gen, e.g. ancestral sequences.

temp.file

temporary file for seqgen output.

Warning(s)

Carefully read the seq-gen's original document before using the seqgen() function.

Author

Rambaut, A. and Grassly, N.C. (1997).

Maintain: Wei-Chen Chen

Details

This function directly reuses the C code of seq-gen by arguments as input from the STDIN. The options opts is followed from the original seq-gen except an input tree.

Input either a rooted.tree or a newick.tree, and rooted.tree should have a Class phylo.

For examples, options commonly used in phyclust are:

• "-m": set an evolution model, e.g. "-mHKY".

• "-t": set transition/transversion ratio, e.g. "-t0.7".

• "-f": equilibrium probabilities of A, C, G, and T, e.g. "-f0.1,0.2,0.3,0.4".

• "-l": length of sequences, e.g. "-l10".

• "-s": scale rate for the total height of input tree, "-s0.2".

• "-k": index of ancestral sequence in input file, see gen.seq.HKY.

These will return sequences in Format phylip which can be read by read.seqgen() and transfered into an object with Class seq.data.

The maximum number of tips is 2000 in seqgen() by default, but an extra option opts = "-u 2014 ..." can be simply increase the size to 2014.

Note:

• input and rooted.tree/newick.tree can not be submitted at the same time.

• seq-gen use the order A, C, G, T.

• -t is ts/tv ratio which is not equal to \(\kappa\).

• See more examples in gen.seq.HKY() and gen.seq.SNP().

temp.file allows users to specify seqgen output file themselves, but this file will not be deleted nor converted into R after the call to seqgen(). Users should take care the readings. By default, seqgen() uses a system temp file to store the output which is converted into R after the call and is deleted after converting.

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

Rambaut, A. and Grassly, N.C. (1997) “Seq-Gen: An Application for the Monte Carlo Simulation of DNA Sequence Evolution along Phylogenetic Trees”, Computer Applications In The Biosciences, 13:3, 235-238. http://tree.bio.ed.ac.uk/software/seqgen/

See Also

print.seqgen(), read.tree(), ms(), gen.seq.HKY(), gen.seq.SNP().

Examples

if (FALSE) {
library(phyclust, quiet = TRUE)

set.seed(123)
ret.ms <- ms(nsam = 5, nreps = 1, opts = "-T")
seqgen(opts = "-mHKY -l40 -s0.2", newick.tree = ret.ms[3])

}