Simulated sequence alignment from the stepwise package
Simulated sequence alignment comprised of 30 sequences, each of length 1000 bases.
A 30-by-1000 matrix of mode character. Each row represents a genetic sequence. Each column is a nucleotide in that genetic sequence.
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).
Graham J, McNeney B and Seillier-Moiseiwitsch F (2004). Stepwise detection of recombination breakpoints in sequence alignments. Bioinformatics Sep 23; [Epub ahead of print]
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
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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)
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