T92: The T92 class

Description

This class implements the T92 GTR-submodel.

The rate parameters are the following: "Alpha", "Beta","Gamma". The theta virtual field stores the GC content parameter.

Package: Class T92

Directly known subclasses:

public static class T92 extends GTR

Usage

T92(name="Anonymous", rate.params=list(Alpha = 1, Beta = 1), theta=0.5, ...)

Arguments

name

Object name.

rate.params

Rate parameters.

theta

GC content (0.5 by default).

...

Not used.

Fields and Methods

Methods:

	`checkConsistency`	-
	`getRateParam`	-
	`getRateParamList`	-
	`getTheta`	-
	`setRateParam`	-
	`setRateParamList`	-
	`setTheta`	-
	`summary`	-

Methods inherited from GTR: checkConsistency, getBaseFreqs, getRateParam, getRateParamList, setBaseFreqs, setRateParam, setRateParamList, summary

Methods inherited from UNREST: checkConsistency, summary

Methods inherited from GeneralSubstitution: as.character, checkConsistency, clone, getAlphabet, getEquDist, getEventRate, getEventRateAtSite, getEventsAtSite, getQMatrix, getRate, getRateList, hasUndefinedRate, is, plot, rescaleQMatrix, sampleState, setAlphabet, setEquDist, setQMatrix, setRate, setRateList, summary

Methods inherited from Process: !=, ==, as.character, checkConsistency, clone, getAlphabet, getEventsAtSite, getId, getName, getParameterAtSite, getSiteSpecificParamIds, getSiteSpecificParamList, getWriteProtected, hasSiteSpecificParameter, hasUndefinedRate, is, setAlphabet, setId, setName, setParameterAtSite, setSiteSpecificParamIds, setSiteSpecificParamList, setWriteProtected, summary

Methods inherited from PSRoot: checkConsistency, enableVirtual, getComments, getMethodsList, globalConsistencyCheck, intersect.list, is, is.na, ll, my.all.equal, plot, setComments, setMethodsList, summary, virtualAssignmentForbidden

Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

References

Tamura, K. (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases - Molecular Biology and Evolution 9:678-687 http://bit.ly/c6Pe0q

Examples

Run this code

# NOT RUN {
	# create substitution process object
       p<-T92(rate.params=list( "Alpha"=10,"Beta"=2),theta=0.8)
       # get a summary
       summary(p)
	# display a bubble plot
	plot(p)

	# The following code demonstrates how to use
	# the process in a simulation.

	# create a sequence, attach process p
	s<-NucleotideSequence(length=20,processes=list(list(p)))
	# sample states
	sampleStates(s)
	# make the first five positions invariable
	setRateMultipliers(s,p,0,1:5)
	# get rate multipliers
	getRateMultipliers(s,p)
	# create a simulation object
	sim<-PhyloSim(root.seq=s,phylo=rcoal(2))
	# run simulation
	Simulate(sim)
	# print alignment
	sim$alignment
 
# }