F81: The F81 class

In phylosim: Flexible Simulations of Biological Sequence Evolution

Description

This class implements the F81 GTR-submodel.

Package:
Class F81

Object
~~|
~~+--PSRoot
~~~~~~~|
~~~~~~~+--Process
~~~~~~~~~~~~|
~~~~~~~~~~~~+--GeneralSubstitution
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--UNREST
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--GTR
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--F81

Directly known subclasses:

public static class F81
extends GTR

Usage

F81(name="Anonymous", base.freqs=c(0.25, 0.25, 0.25, 0.25), ...)

Arguments

name	Object name.
base.freqs	Base frequency parameters.
...	Not used.

Fields and Methods

Methods:

	checkConsistency	-
	getBaseFreqs	-
	getRateParam	-
	getRateParamList	-
	setBaseFreqs	-
	setRateParam	-
	setRateParamList	-
	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

Author(s)

Botond Sipos, Gregory Jordan

References

Felsenstein, J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach - Journal of Molecular Evolution 17:368-376 http://dx.doi.org/10.1007/BF01734359

See Also

GTR UNREST GeneralSubstitution HKY

Examples

	# create substitution process object
       p<-F81(base.freqs=c(1,2,3,4)/10)
       # 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
 

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