saveAlignment.PhyloSim: Save the alignment stored in a PhyloSim object in a Fasta...
In phylosim: Flexible Simulations of Biological Sequence Evolution

Description Usage Arguments Value Author(s) See Also Examples

Save the alignment stored in a PhyloSim object in a Fasta file.

1 2	## S3 method for class 'PhyloSim' saveAlignment(this, file="phylosim.fas", skip.internal=FALSE, paranoid=FALSE, ...)

`this`	A PhyloSim object.
`file`	The name of the output file.
`skip.internal`	Do not save sequences corresponding to internal nodes.
`paranoid`	Check the consistency of the alignment.
`...`	Not used.

The PhyloSim object (invisible).

Botond Sipos, Gregory Jordan

For more information see PhyloSim.

	# Create a PhyloSim object.
	# Provide the phylo object
	# and the root sequence.
	sim<-PhyloSim(
		name="TinySim",
		phylo=rcoal(3),
		root.seq=NucleotideSequence(string="ATG",processes=list(list(JC69())))
	);
	# run the simulation
	Simulate(sim)
	# save the alignment
	file<-paste("PhyloSim_dummy_fasta_",Sys.getpid(),".fas",sep="");
	saveAlignment(sim,file=file,paranoid=TRUE);
	# print out the Fasta file
	cat(paste(scan(file=file,what=character(),sep="\n"),collapse="\n"));cat("\n");
	# delete Fasta file
	unlink(file);