phylosim (version 3.0.5)

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

Description

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

Usage

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

Arguments

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.

Value

The PhyloSim object (invisible).

See Also

For more information see PhyloSim.

Examples

# NOT RUN {
	# 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);
 
# }