getAlignment.PhyloSim: Get the alignment stored in a PhyloSim object

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

Get the alignment stored in a PhyloSim object.

Usage

## S3 method for class 'PhyloSim'
getAlignment(this, ...)

Arguments

this	A PhyloSim object.
...	Not used.

Value

The alignment as a matrix. Gap are represented by strings composed of dashes.

Author(s)

Botond Sipos, Gregory Jordan

See Also

For more information see PhyloSim.

Examples

	# 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)
	# get the resulting aligment
	getAlignment(sim)
	# via virtual fileld:
	sim$alignment
 

phylosim documentation built on Nov. 22, 2019, 1:07 a.m.