stepwise (version 0.3)

stepwise.seqs: Simulated sequence alignment from the stepwise package

Description

Simulated sequence alignment comprised of 30 sequences, each of length 1000 bases.

Usage

data(stepwise.seqs)

Format

A 30-by-1000 matrix of mode character. Each row represents a genetic sequence. Each column is a nucleotide in that genetic sequence.

Source

Graham J, McNeney B and Seillier-Moiseiwitsch F (2004). Stepwise detection of recombination breakpoints in sequence alignments. Bioinformatics Sep 23; [Epub ahead of print]

Details

A simulated data set analysed by Graham et al. (2004) to illustrate the stepwise recombination detection methods. The alignment was simulated using Treevolve version 1.3 (Grassly and Holmes 1997). For details on the parameter values used in the simulation, see Graham et al. (2004).

References

Grassley NC and Holmes EC (1997). A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol, 14(3): 239-247

Examples

data(stepwise.seqs) 
dim(stepwise.seqs) # 30 x 1000
## Not run: 
# # write the 30 sequences to a Phylip-format input file 
# cat(paste(nrow(stepwise.seqs),ncol(stepwise.seqs),"\n"),
# file="stepwise.phy")
# write.table(stepwise.seqs,file="stepwise.phy",append=TRUE,quote=FALSE,
# sep="", row.names=TRUE,col.names=FALSE)
# ## End(Not run)