!=.Alphabet	000==.Alphabet
!=.Process	000==.Process
==,Alphabet-method	000==.Alphabet
==,Process-method	000==.Process
==.Alphabet	000==.Alphabet
==.Process	000==.Process
all	Undocumented.PhyloSim
Alphabet	Alphabet
Alphabet.==	000==.Alphabet
Alphabet.as.character	as.character.Alphabet
Alphabet.checkConsistency	checkConsistency.Alphabet
Alphabet.getSize	getSize.Alphabet
Alphabet.getSymbolLength	getSymbolLength.Alphabet
Alphabet.getSymbols	getSymbols.Alphabet
Alphabet.getType	getType.Alphabet
Alphabet.getWriteProtected	getWriteProtected.Alphabet
Alphabet.hasSymbols	hasSymbols.Alphabet
Alphabet.isEmpty	isEmpty.Alphabet
Alphabet.setSize	setSize.Alphabet
Alphabet.setSymbolLength	setSymbolLength.Alphabet
Alphabet.setSymbols	setSymbols.Alphabet
Alphabet.setType	setType.Alphabet
Alphabet.setWriteProtected	setWriteProtected.Alphabet
Alphabet.summary	summary.Alphabet
AminoAcidAlphabet	AminoAcidAlphabet
AminoAcidSequence	AminoAcidSequence
AminoAcidSubst	AminoAcidSubst
AminoAcidSubst.buildFromPAML	buildFromPAML.AminoAcidSubst
AminoAcidSubst.checkConsistency	checkConsistency.AminoAcidSubst
AminoAcidSubst.newAAMatrix	newAAMatrix.AminoAcidSubst
AminoAcidSubst.summary	summary.AminoAcidSubst
AnyAlphabet	AnyAlphabet
areSynonymous	Undocumented.PhyloSim
areSynonymous,CodonAlphabet-method	areSynonymous.CodonAlphabet
areSynonymous.CodonAlphabet	areSynonymous.CodonAlphabet
as.character,Alphabet-method	as.character.Alphabet
as.character,Event-method	as.character.Event
as.character,GeneralSubstitution-method	as.character.GeneralSubstitution
as.character,PhyloSim-method	as.character.PhyloSim
as.character,Process-method	as.character.Process
as.character,QMatrix-method	as.character.QMatrix
as.character,Sequence-method	as.character.Sequence
as.character,Site-method	as.character.Site
as.character,ToleranceSubstitution-method	as.character.ToleranceSubstitution
as.character.Alphabet	as.character.Alphabet
as.character.Event	as.character.Event
as.character.GeneralSubstitution	as.character.GeneralSubstitution
as.character.PhyloSim	as.character.PhyloSim
as.character.Process	as.character.Process
as.character.QMatrix	as.character.QMatrix
as.character.Sequence	as.character.Sequence
as.character.Site	as.character.Site
as.character.ToleranceSubstitution	as.character.ToleranceSubstitution
attachHookToNode	Undocumented.PhyloSim
attachHookToNode,PhyloSim-method	attachHookToNode.PhyloSim
attachHookToNode.PhyloSim	attachHookToNode.PhyloSim
attachProcess	Undocumented.PhyloSim
attachProcess,Sequence-method	attachProcess.Sequence
attachProcess,Site-method	attachProcess.Site
attachProcess.Sequence	attachProcess.Sequence
attachProcess.Site	attachProcess.Site
attachSeqToNode	Undocumented.PhyloSim
attachSeqToNode,PhyloSim-method	attachSeqToNode.PhyloSim
attachSeqToNode.PhyloSim	attachSeqToNode.PhyloSim
BinaryAlphabet	BinaryAlphabet
BinarySequence	BinarySequence
BinarySubst	BinarySubst
BinarySubst.checkConsistency	checkConsistency.BinarySubst
BinarySubst.summary	summary.BinarySubst
BrownianInsertor	BrownianInsertor
BrownianInsertor.BrownianPath	BrownianPath.BrownianInsertor
BrownianInsertor.checkConsistency	checkConsistency.BrownianInsertor
BrownianInsertor.getScale	getScale.BrownianInsertor
BrownianInsertor.getType	getType.BrownianInsertor
BrownianInsertor.setScale	setScale.BrownianInsertor
BrownianInsertor.setType	setType.BrownianInsertor
BrownianInsertor.summary	summary.BrownianInsertor
BrownianPath	Undocumented.PhyloSim
BrownianPath,BrownianInsertor-method	BrownianPath.BrownianInsertor
BrownianPath.BrownianInsertor	BrownianPath.BrownianInsertor
buildFromPAML	Undocumented.PhyloSim
buildFromPAML,AminoAcidSubst-method	buildFromPAML.AminoAcidSubst
buildFromPAML,CodonSubst-method	buildFromPAML.CodonSubst
buildFromPAML.AminoAcidSubst	buildFromPAML.AminoAcidSubst
buildFromPAML.CodonSubst	buildFromPAML.CodonSubst
checkConsistency	Undocumented.PhyloSim
checkConsistency,Alphabet-method	checkConsistency.Alphabet
checkConsistency,AminoAcidSubst-method	checkConsistency.AminoAcidSubst
checkConsistency,BinarySubst-method	checkConsistency.BinarySubst
checkConsistency,BrownianInsertor-method	checkConsistency.BrownianInsertor
checkConsistency,CodonAlphabet-method	checkConsistency.CodonAlphabet
checkConsistency,CodonSequence-method	checkConsistency.CodonSequence
checkConsistency,CodonSubst-method	checkConsistency.CodonSubst
checkConsistency,CodonUNREST-method	checkConsistency.CodonUNREST
checkConsistency,ContinuousDeletor-method	checkConsistency.ContinuousDeletor
checkConsistency,ContinuousInsertor-method	checkConsistency.ContinuousInsertor
checkConsistency,DiscreteDeletor-method	checkConsistency.DiscreteDeletor
checkConsistency,DiscreteInsertor-method	checkConsistency.DiscreteInsertor
checkConsistency,Event-method	checkConsistency.Event
checkConsistency,F81-method	checkConsistency.F81
checkConsistency,F84-method	checkConsistency.F84
checkConsistency,FastFieldDeletor-method	checkConsistency.FastFieldDeletor
checkConsistency,GeneralDeletor-method	checkConsistency.GeneralDeletor
checkConsistency,GeneralInDel-method	checkConsistency.GeneralInDel
checkConsistency,GeneralInsertor-method	checkConsistency.GeneralInsertor
checkConsistency,GeneralSubstitution-method	checkConsistency.GeneralSubstitution
checkConsistency,GTR-method	checkConsistency.GTR
checkConsistency,GY94-method	checkConsistency.GY94
checkConsistency,HKY-method	checkConsistency.HKY
checkConsistency,JC69-method	checkConsistency.JC69
checkConsistency,K80-method	checkConsistency.K80
checkConsistency,K81-method	checkConsistency.K81
checkConsistency,PhyloSim-method	checkConsistency.PhyloSim
checkConsistency,Process-method	checkConsistency.Process
checkConsistency,PSRoot-method	checkConsistency.PSRoot
checkConsistency,PSRootSummary-method	checkConsistency.PSRootSummary
checkConsistency,QMatrix-method	checkConsistency.QMatrix
checkConsistency,Sequence-method	checkConsistency.Sequence
checkConsistency,Site-method	checkConsistency.Site
checkConsistency,T92-method	checkConsistency.T92
checkConsistency,TN93-method	checkConsistency.TN93
checkConsistency,ToleranceSubstitution-method	checkConsistency.ToleranceSubstitution
checkConsistency,UNREST-method	checkConsistency.UNREST
checkConsistency.Alphabet	checkConsistency.Alphabet
checkConsistency.AminoAcidSubst	checkConsistency.AminoAcidSubst
checkConsistency.BinarySubst	checkConsistency.BinarySubst
checkConsistency.BrownianInsertor	checkConsistency.BrownianInsertor
checkConsistency.CodonAlphabet	checkConsistency.CodonAlphabet
checkConsistency.CodonSequence	checkConsistency.CodonSequence
checkConsistency.CodonSubst	checkConsistency.CodonSubst
checkConsistency.CodonUNREST	checkConsistency.CodonUNREST
checkConsistency.ContinuousDeletor	checkConsistency.ContinuousDeletor
checkConsistency.ContinuousInsertor	checkConsistency.ContinuousInsertor
checkConsistency.DiscreteDeletor	checkConsistency.DiscreteDeletor
checkConsistency.DiscreteInsertor	checkConsistency.DiscreteInsertor
checkConsistency.Event	checkConsistency.Event
checkConsistency.F81	checkConsistency.F81
checkConsistency.F84	checkConsistency.F84
checkConsistency.FastFieldDeletor	checkConsistency.FastFieldDeletor
checkConsistency.GeneralDeletor	checkConsistency.GeneralDeletor
checkConsistency.GeneralInDel	checkConsistency.GeneralInDel
checkConsistency.GeneralInsertor	checkConsistency.GeneralInsertor
checkConsistency.GeneralSubstitution	checkConsistency.GeneralSubstitution
checkConsistency.GTR	checkConsistency.GTR
checkConsistency.GY94	checkConsistency.GY94
checkConsistency.HKY	checkConsistency.HKY
checkConsistency.JC69	checkConsistency.JC69
checkConsistency.K80	checkConsistency.K80
checkConsistency.K81	checkConsistency.K81
checkConsistency.PhyloSim	checkConsistency.PhyloSim
checkConsistency.Process	checkConsistency.Process
checkConsistency.PSRoot	checkConsistency.PSRoot
checkConsistency.PSRootSummary	checkConsistency.PSRootSummary
checkConsistency.QMatrix	checkConsistency.QMatrix
checkConsistency.Sequence	checkConsistency.Sequence
checkConsistency.Site	checkConsistency.Site
checkConsistency.T92	checkConsistency.T92
checkConsistency.TN93	checkConsistency.TN93
checkConsistency.ToleranceSubstitution	checkConsistency.ToleranceSubstitution
checkConsistency.UNREST	checkConsistency.UNREST
clearStates	Undocumented.PhyloSim
clearStates,Sequence-method	clearStates.Sequence
clearStates.Sequence	clearStates.Sequence
clone,GeneralSubstitution-method	clone.GeneralSubstitution
clone,Process-method	clone.Process
clone,Sequence-method	clone.Sequence
clone,ToleranceSubstitution-method	clone.ToleranceSubstitution
clone.GeneralSubstitution	clone.GeneralSubstitution
clone.Process	clone.Process
clone.Sequence	clone.Sequence
clone.ToleranceSubstitution	clone.ToleranceSubstitution
CodonAlphabet	CodonAlphabet
CodonAlphabet.areSynonymous	areSynonymous.CodonAlphabet
CodonAlphabet.checkConsistency	checkConsistency.CodonAlphabet
CodonAlphabet.getTableId	getTableId.CodonAlphabet
CodonAlphabet.getTransTable	getTransTable.CodonAlphabet
CodonAlphabet.isStartCodon	isStartCodon.CodonAlphabet
CodonAlphabet.isStopCodon	isStopCodon.CodonAlphabet
CodonAlphabet.setTableId	setTableId.CodonAlphabet
CodonAlphabet.setTransTable	setTransTable.CodonAlphabet
CodonAlphabet.summary	summary.CodonAlphabet
CodonAlphabet.translateCodon	translateCodon.CodonAlphabet
CodonSequence	CodonSequence
CodonSequence.checkConsistency	checkConsistency.CodonSequence
CodonSequence.getOmegas	getOmegas.CodonSequence
CodonSequence.omegaHist	omegaHist.CodonSequence
CodonSequence.omegaVarM0	omegaVarM0.CodonSequence
CodonSequence.omegaVarM1	omegaVarM1.CodonSequence
CodonSequence.omegaVarM2	omegaVarM2.CodonSequence
CodonSequence.omegaVarM3	omegaVarM3.CodonSequence
CodonSequence.omegaVarM4	omegaVarM4.CodonSequence
CodonSequence.setOmegas	setOmegas.CodonSequence
CodonSequence.Translate	Translate.CodonSequence
CodonSubst	CodonSubst
CodonSubst.buildFromPAML	buildFromPAML.CodonSubst
CodonSubst.checkConsistency	checkConsistency.CodonSubst
CodonSubst.newMatrix	newMatrix.CodonSubst
CodonSubst.summary	summary.CodonSubst
CodonUNREST	CodonUNREST
CodonUNREST.checkConsistency	checkConsistency.CodonUNREST
ContinuousDeletor	ContinuousDeletor
ContinuousDeletor.checkConsistency	checkConsistency.ContinuousDeletor
ContinuousDeletor.getDist	getDist.ContinuousDeletor
ContinuousDeletor.getMaxLength	getMaxLength.ContinuousDeletor
ContinuousDeletor.plot	plot.ContinuousDeletor
ContinuousDeletor.setDist	setDist.ContinuousDeletor
ContinuousDeletor.setMaxLength	setMaxLength.ContinuousDeletor
ContinuousDeletor.summary	summary.ContinuousDeletor
ContinuousInsertor	ContinuousInsertor
ContinuousInsertor.checkConsistency	checkConsistency.ContinuousInsertor
ContinuousInsertor.getDist	getDist.ContinuousInsertor
ContinuousInsertor.getMaxLength	getMaxLength.ContinuousInsertor
ContinuousInsertor.plot	plot.ContinuousInsertor
ContinuousInsertor.setDist	setDist.ContinuousInsertor
ContinuousInsertor.setMaxLength	setMaxLength.ContinuousInsertor
ContinuousInsertor.summary	summary.ContinuousInsertor
copySubSequence	Undocumented.PhyloSim
copySubSequence,Sequence-method	copySubSequence.Sequence
copySubSequence.Sequence	copySubSequence.Sequence
cpREV	cpREV
Debug	Undocumented.PhyloSim
Debug,PhyloSim-method	Debug.PhyloSim
Debug.PhyloSim	Debug.PhyloSim
default	Undocumented.PhyloSim
deleteSubSequence	Undocumented.PhyloSim
deleteSubSequence,Sequence-method	deleteSubSequence.Sequence
deleteSubSequence.Sequence	deleteSubSequence.Sequence
detachHookFromNode	Undocumented.PhyloSim
detachHookFromNode,PhyloSim-method	detachHookFromNode.PhyloSim
detachHookFromNode.PhyloSim	detachHookFromNode.PhyloSim
detachProcess	Undocumented.PhyloSim
detachProcess,Sequence-method	detachProcess.Sequence
detachProcess,Site-method	detachProcess.Site
detachProcess.Sequence	detachProcess.Sequence
detachProcess.Site	detachProcess.Site
detachSeqFromNode	Undocumented.PhyloSim
detachSeqFromNode,PhyloSim-method	detachSeqFromNode.PhyloSim
detachSeqFromNode.PhyloSim	detachSeqFromNode.PhyloSim
DiscreteDeletor	DiscreteDeletor
DiscreteDeletor.checkConsistency	checkConsistency.DiscreteDeletor
DiscreteDeletor.getProbs	getProbs.DiscreteDeletor
DiscreteDeletor.getSizes	getSizes.DiscreteDeletor
DiscreteDeletor.plot	plot.DiscreteDeletor
DiscreteDeletor.setProbs	setProbs.DiscreteDeletor
DiscreteDeletor.setSizes	setSizes.DiscreteDeletor
DiscreteDeletor.summary	summary.DiscreteDeletor
DiscreteInsertor	DiscreteInsertor
DiscreteInsertor.checkConsistency	checkConsistency.DiscreteInsertor
DiscreteInsertor.getProbs	getProbs.DiscreteInsertor
DiscreteInsertor.getSizes	getSizes.DiscreteInsertor
DiscreteInsertor.plot	plot.DiscreteInsertor
DiscreteInsertor.setProbs	setProbs.DiscreteInsertor
DiscreteInsertor.setSizes	setSizes.DiscreteInsertor
DiscreteInsertor.summary	summary.DiscreteInsertor
ECMrest	ECMrest
ECMunrest	ECMunrest
enableVirtual	Undocumented.PhyloSim
enableVirtual,PSRoot-method	enableVirtual.PSRoot
enableVirtual.PSRoot	enableVirtual.PSRoot
equal	Undocumented.PhyloSim
Event	Event
Event.as.character	as.character.Event
Event.checkConsistency	checkConsistency.Event
Event.getHandler	getHandler.Event
Event.getName	getName.Event
Event.getPosition	getPosition.Event
Event.getProcess	getProcess.Event
Event.getRate	getRate.Event
Event.getSite	getSite.Event
Event.getWriteProtected	getWriteProtected.Event
Event.Perform	Perform.Event
Event.setHandler	setHandler.Event
Event.setName	setName.Event
Event.setPosition	setPosition.Event
Event.setProcess	setProcess.Event
Event.setRate	setRate.Event
Event.setSite	setSite.Event
Event.setWriteProtected	setWriteProtected.Event
Event.summary	summary.Event
exportStatTree	Undocumented.PhyloSim
exportStatTree,PhyloSim-method	exportStatTree.PhyloSim
exportStatTree.PhyloSim	exportStatTree.PhyloSim
F81	F81
F81.checkConsistency	checkConsistency.F81
F81.getBaseFreqs	getBaseFreqs.F81
F81.getRateParam	getRateParam.F81
F81.getRateParamList	getRateParamList.F81
F81.setBaseFreqs	setBaseFreqs.F81
F81.setRateParam	setRateParam.F81
F81.setRateParamList	setRateParamList.F81
F81.summary	summary.F81
F84	F84
F84.checkConsistency	checkConsistency.F84
F84.getBaseFreqs	getBaseFreqs.F84
F84.getKappa	getKappa.F84
F84.getRateParam	getRateParam.F84
F84.getRateParamList	getRateParamList.F84
F84.setBaseFreqs	setBaseFreqs.F84
F84.setKappa	setKappa.F84
F84.setRateParam	setRateParam.F84
F84.setRateParamList	setRateParamList.F84
F84.summary	summary.F84
FastFieldDeletor	FastFieldDeletor
FastFieldDeletor.checkConsistency	checkConsistency.FastFieldDeletor
FastFieldDeletor.getEventsAtSite	getEventsAtSite.FastFieldDeletor
FastFieldDeletor.getLengthParam1	getLengthParam1.FastFieldDeletor
FastFieldDeletor.getLengthParam2	getLengthParam2.FastFieldDeletor
FastFieldDeletor.getToleranceMargin	getToleranceMargin.FastFieldDeletor
FastFieldDeletor.getType	getType.FastFieldDeletor
FastFieldDeletor.setLengthParam1	setLengthParam1.FastFieldDeletor
FastFieldDeletor.setLengthParam2	setLengthParam2.FastFieldDeletor
FastFieldDeletor.setToleranceMargin	setToleranceMargin.FastFieldDeletor
FastFieldDeletor.setType	setType.FastFieldDeletor
FastFieldDeletor.summary	summary.FastFieldDeletor
flagTotalRate	Undocumented.PhyloSim
flagTotalRate,Site-method	flagTotalRate.Site
flagTotalRate.Site	flagTotalRate.Site
GeneralDeletor	GeneralDeletor
GeneralDeletor.checkConsistency	checkConsistency.GeneralDeletor
GeneralDeletor.getEventsAtSite	getEventsAtSite.GeneralDeletor
GeneralDeletor.summary	summary.GeneralDeletor
GeneralInDel	GeneralInDel
GeneralInDel.checkConsistency	checkConsistency.GeneralInDel
GeneralInDel.getAcceptBy	getAcceptBy.GeneralInDel
GeneralInDel.getProposeBy	getProposeBy.GeneralInDel
GeneralInDel.getRate	getRate.GeneralInDel
GeneralInDel.hasUndefinedRate	hasUndefinedRate.GeneralInDel
GeneralInDel.proposeLength	proposeLength.GeneralInDel
GeneralInDel.setAcceptBy	setAcceptBy.GeneralInDel
GeneralInDel.setProposeBy	setProposeBy.GeneralInDel
GeneralInDel.setRate	setRate.GeneralInDel
GeneralInDel.summary	summary.GeneralInDel
GeneralInsertor	GeneralInsertor
GeneralInsertor.checkConsistency	checkConsistency.GeneralInsertor
GeneralInsertor.generateInsert	generateInsert.GeneralInsertor
GeneralInsertor.getAcceptWin	getAcceptWin.GeneralInsertor
GeneralInsertor.getEventsAtSite	getEventsAtSite.GeneralInsertor
GeneralInsertor.getGenerateBy	getGenerateBy.GeneralInsertor
GeneralInsertor.getInsertHook	getInsertHook.GeneralInsertor
GeneralInsertor.getTemplateSeq	getTemplateSeq.GeneralInsertor
GeneralInsertor.setAcceptWin	setAcceptWin.GeneralInsertor
GeneralInsertor.setGenerateBy	setGenerateBy.GeneralInsertor
GeneralInsertor.setInsertHook	setInsertHook.GeneralInsertor
GeneralInsertor.setTemplateSeq	setTemplateSeq.GeneralInsertor
GeneralInsertor.summary	summary.GeneralInsertor
GeneralSubstitution	GeneralSubstitution
GeneralSubstitution.as.character	as.character.GeneralSubstitution
GeneralSubstitution.checkConsistency	checkConsistency.GeneralSubstitution
GeneralSubstitution.clone	clone.GeneralSubstitution
GeneralSubstitution.getAlphabet	getAlphabet.GeneralSubstitution
GeneralSubstitution.getEquDist	getEquDist.GeneralSubstitution
GeneralSubstitution.getEventRate	getEventRate.GeneralSubstitution
GeneralSubstitution.getEventRateAtSite	getEventRateAtSite.GeneralSubstitution
GeneralSubstitution.getEventsAtSite	getEventsAtSite.GeneralSubstitution
GeneralSubstitution.getQMatrix	getQMatrix.GeneralSubstitution
GeneralSubstitution.getRate	getRate.GeneralSubstitution
GeneralSubstitution.getRateList	getRateList.GeneralSubstitution
GeneralSubstitution.hasUndefinedRate	hasUndefinedRate.GeneralSubstitution
GeneralSubstitution.plot	plot.GeneralSubstitution
GeneralSubstitution.rescaleQMatrix	rescaleQMatrix.GeneralSubstitution
GeneralSubstitution.sampleState	sampleState.GeneralSubstitution
GeneralSubstitution.setAlphabet	setAlphabet.GeneralSubstitution
GeneralSubstitution.setEquDist	setEquDist.GeneralSubstitution
GeneralSubstitution.setQMatrix	setQMatrix.GeneralSubstitution
GeneralSubstitution.setRate	setRate.GeneralSubstitution
GeneralSubstitution.setRateList	setRateList.GeneralSubstitution
GeneralSubstitution.summary	summary.GeneralSubstitution
generateInsert	Undocumented.PhyloSim
generateInsert,GeneralInsertor-method	generateInsert.GeneralInsertor
generateInsert.GeneralInsertor	generateInsert.GeneralInsertor
getAcceptBy	Undocumented.PhyloSim
getAcceptBy,GeneralInDel-method	getAcceptBy.GeneralInDel
getAcceptBy.GeneralInDel	getAcceptBy.GeneralInDel
getAcceptBy.GeneralInsertor	getAcceptBy.GeneralInDel
getAcceptWin	Undocumented.PhyloSim
getAcceptWin,GeneralInsertor-method	getAcceptWin.GeneralInsertor
getAcceptWin.GeneralInsertor	getAcceptWin.GeneralInsertor
getAlignment	Undocumented.PhyloSim
getAlignment,PhyloSim-method	getAlignment.PhyloSim
getAlignment.PhyloSim	getAlignment.PhyloSim
getAlignmentLength	Undocumented.PhyloSim
getAlignmentLength,PhyloSim-method	getAlignmentLength.PhyloSim
getAlignmentLength.PhyloSim	getAlignmentLength.PhyloSim
getAlphabet	Undocumented.PhyloSim
getAlphabet,GeneralSubstitution-method	getAlphabet.GeneralSubstitution
getAlphabet,Process-method	getAlphabet.Process
getAlphabet,QMatrix-method	getAlphabet.QMatrix
getAlphabet,Site-method	getAlphabet.Site
getAlphabet,ToleranceSubstitution-method	getAlphabet.ToleranceSubstitution
getAlphabet.GeneralSubstitution	getAlphabet.GeneralSubstitution
getAlphabet.Process	getAlphabet.Process
getAlphabet.QMatrix	getAlphabet.QMatrix
getAlphabet.Site	getAlphabet.Site
getAlphabet.ToleranceSubstitution	getAlphabet.ToleranceSubstitution
getAlphabets	Undocumented.PhyloSim
getAlphabets,Sequence-method	getAlphabets.Sequence
getAlphabets.Sequence	getAlphabets.Sequence
getAncestral	Undocumented.PhyloSim
getAncestral,Sequence-method	getAncestral.Sequence
getAncestral,Site-method	getAncestral.Site
getAncestral.Sequence	getAncestral.Sequence
getAncestral.Site	getAncestral.Site
getBaseFreqs	Undocumented.PhyloSim
getBaseFreqs,F81-method	getBaseFreqs.F81
getBaseFreqs,F84-method	getBaseFreqs.F84
getBaseFreqs,GTR-method	getBaseFreqs.GTR
getBaseFreqs,HKY-method	getBaseFreqs.HKY
getBaseFreqs,K80-method	getBaseFreqs.K80
getBaseFreqs,K81-method	getBaseFreqs.K81
getBaseFreqs,TN93-method	getBaseFreqs.TN93
getBaseFreqs.F81	getBaseFreqs.F81
getBaseFreqs.F84	getBaseFreqs.F84
getBaseFreqs.GTR	getBaseFreqs.GTR
getBaseFreqs.HKY	getBaseFreqs.HKY
getBaseFreqs.K80	getBaseFreqs.K80
getBaseFreqs.K81	getBaseFreqs.K81
getBaseFreqs.TN93	getBaseFreqs.TN93
getBigRate	Undocumented.PhyloSim
getBigRate,Sequence-method	getBigRate.Sequence
getBigRate.Sequence	getBigRate.Sequence
getBranchEvents	Undocumented.PhyloSim
getBranchEvents,PhyloSim-method	getBranchEvents.PhyloSim
getBranchEvents.PhyloSim	getBranchEvents.PhyloSim
getCodonFreqs	Undocumented.PhyloSim
getCodonFreqs,GY94-method	getCodonFreqs.GY94
getCodonFreqs.GY94	getCodonFreqs.GY94
getComments	Undocumented.PhyloSim
getComments,PSRoot-method	getComments.PSRoot
getComments.PSRoot	getComments.PSRoot
getCumulativeRates	Undocumented.PhyloSim
getCumulativeRates,Sequence-method	getCumulativeRates.Sequence
getCumulativeRates.Sequence	getCumulativeRates.Sequence
getCumulativeRatesFromRange	Undocumented.PhyloSim
getCumulativeRatesFromRange,Sequence-method	getCumulativeRatesFromRange.Sequence
getCumulativeRatesFromRange.Sequence	getCumulativeRatesFromRange.Sequence
getDeletionTolerance	Undocumented.PhyloSim
getDeletionTolerance,Sequence-method	getDeletionTolerance.Sequence
getDeletionTolerance.Sequence	getDeletionTolerance.Sequence
getDist	Undocumented.PhyloSim
getDist,ContinuousDeletor-method	getDist.ContinuousDeletor
getDist,ContinuousInsertor-method	getDist.ContinuousInsertor
getDist.ContinuousDeletor	getDist.ContinuousDeletor
getDist.ContinuousInsertor	getDist.ContinuousInsertor
getEdge	Undocumented.PhyloSim
getEdge,PhyloSim-method	getEdge.PhyloSim
getEdge.PhyloSim	getEdge.PhyloSim
getEdges	Undocumented.PhyloSim
getEdges,PhyloSim-method	getEdges.PhyloSim
getEdges.PhyloSim	getEdges.PhyloSim
getEquDist	Undocumented.PhyloSim
getEquDist,GeneralSubstitution-method	getEquDist.GeneralSubstitution
getEquDist,ToleranceSubstitution-method	getEquDist.ToleranceSubstitution
getEquDist.GeneralSubstitution	getEquDist.GeneralSubstitution
getEquDist.ToleranceSubstitution	getEquDist.ToleranceSubstitution
getEventRate	Undocumented.PhyloSim
getEventRate,GeneralSubstitution-method	getEventRate.GeneralSubstitution
getEventRate,QMatrix-method	getEventRate.QMatrix
getEventRate,ToleranceSubstitution-method	getEventRate.ToleranceSubstitution
getEventRate.GeneralSubstitution	getEventRate.GeneralSubstitution
getEventRate.QMatrix	getEventRate.QMatrix
getEventRate.ToleranceSubstitution	getEventRate.ToleranceSubstitution
getEventRateAtSite	Undocumented.PhyloSim
getEventRateAtSite,GeneralSubstitution-method	getEventRateAtSite.GeneralSubstitution
getEventRateAtSite,ToleranceSubstitution-method	getEventRateAtSite.ToleranceSubstitution
getEventRateAtSite.GeneralSubstitution	getEventRateAtSite.GeneralSubstitution
getEventRateAtSite.ToleranceSubstitution	getEventRateAtSite.ToleranceSubstitution
getEvents	Undocumented.PhyloSim
getEvents,Sequence-method	getEvents.Sequence
getEvents,Site-method	getEvents.Site
getEvents.Sequence	getEvents.Sequence
getEvents.Site	getEvents.Site
getEventsAtSite	Undocumented.PhyloSim
getEventsAtSite,FastFieldDeletor-method	getEventsAtSite.FastFieldDeletor
getEventsAtSite,GeneralDeletor-method	getEventsAtSite.GeneralDeletor
getEventsAtSite,GeneralInsertor-method	getEventsAtSite.GeneralInsertor
getEventsAtSite,GeneralSubstitution-method	getEventsAtSite.GeneralSubstitution
getEventsAtSite,GY94-method	getEventsAtSite.GY94
getEventsAtSite,Process-method	getEventsAtSite.Process
getEventsAtSite,ToleranceSubstitution-method	getEventsAtSite.ToleranceSubstitution
getEventsAtSite.FastFieldDeletor	getEventsAtSite.FastFieldDeletor
getEventsAtSite.GeneralDeletor	getEventsAtSite.GeneralDeletor
getEventsAtSite.GeneralInsertor	getEventsAtSite.GeneralInsertor
getEventsAtSite.GeneralSubstitution	getEventsAtSite.GeneralSubstitution
getEventsAtSite.GY94	getEventsAtSite.GY94
getEventsAtSite.Process	getEventsAtSite.Process
getEventsAtSite.ToleranceSubstitution	getEventsAtSite.ToleranceSubstitution
getGenerateBy	Undocumented.PhyloSim
getGenerateBy,GeneralInsertor-method	getGenerateBy.GeneralInsertor
getGenerateBy.GeneralInsertor	getGenerateBy.GeneralInsertor
getHandler	Undocumented.PhyloSim
getHandler,Event-method	getHandler.Event
getHandler.Event	getHandler.Event
getId	Undocumented.PhyloSim
getId,PhyloSim-method	getId.PhyloSim
getId,Process-method	getId.Process
getId,QMatrix-method	getId.QMatrix
getId,Sequence-method	getId.Sequence
getId.PhyloSim	getId.PhyloSim
getId.Process	getId.Process
getId.QMatrix	getId.QMatrix
getId.Sequence	getId.Sequence
getInsertHook	Undocumented.PhyloSim
getInsertHook,GeneralInsertor-method	getInsertHook.GeneralInsertor
getInsertHook.GeneralInsertor	getInsertHook.GeneralInsertor
getInsertionTolerance	Undocumented.PhyloSim
getInsertionTolerance,Sequence-method	getInsertionTolerance.Sequence
getInsertionTolerance.Sequence	getInsertionTolerance.Sequence
getKappa	Undocumented.PhyloSim
getKappa,F84-method	getKappa.F84
getKappa,GY94-method	getKappa.GY94
getKappa.F84	getKappa.F84
getKappa.GY94	getKappa.GY94
getLength	Undocumented.PhyloSim
getLength,Sequence-method	getLength.Sequence
getLength.Sequence	getLength.Sequence
getLengthParam1	Undocumented.PhyloSim
getLengthParam1,FastFieldDeletor-method	getLengthParam1.FastFieldDeletor
getLengthParam1.FastFieldDeletor	getLengthParam1.FastFieldDeletor
getLengthParam2	Undocumented.PhyloSim
getLengthParam2,FastFieldDeletor-method	getLengthParam2.FastFieldDeletor
getLengthParam2.FastFieldDeletor	getLengthParam2.FastFieldDeletor
getLogFile	Undocumented.PhyloSim
getLogFile,PhyloSim-method	getLogFile.PhyloSim
getLogFile.PhyloSim	getLogFile.PhyloSim
getLogLevel	Undocumented.PhyloSim
getLogLevel,PhyloSim-method	getLogLevel.PhyloSim
getLogLevel.PhyloSim	getLogLevel.PhyloSim
getMatrix	Undocumented.PhyloSim
getMatrix,QMatrix-method	getMatrix.QMatrix
getMatrix.QMatrix	getMatrix.QMatrix
getMaxLength	Undocumented.PhyloSim
getMaxLength,ContinuousDeletor-method	getMaxLength.ContinuousDeletor
getMaxLength,ContinuousInsertor-method	getMaxLength.ContinuousInsertor
getMaxLength.ContinuousDeletor	getMaxLength.ContinuousDeletor
getMaxLength.ContinuousInsertor	getMaxLength.ContinuousInsertor
getMethodsList	Undocumented.PhyloSim
getMethodsList,PSRoot-method	getMethodsList.PSRoot
getMethodsList.PSRoot	getMethodsList.PSRoot
getName,Event-method	getName.Event
getName,PhyloSim-method	getName.PhyloSim
getName,Process-method	getName.Process
getName,QMatrix-method	getName.QMatrix
getName,Sequence-method	getName.Sequence
getName.Event	getName.Event
getName.PhyloSim	getName.PhyloSim
getName.Process	getName.Process
getName.QMatrix	getName.QMatrix
getName.Sequence	getName.Sequence
getNedges	Undocumented.PhyloSim
getNedges,PhyloSim-method	getNedges.PhyloSim
getNedges.PhyloSim	getNedges.PhyloSim
getNodes	Undocumented.PhyloSim
getNodes,PhyloSim-method	getNodes.PhyloSim
getNodes.PhyloSim	getNodes.PhyloSim
getNtips	Undocumented.PhyloSim
getNtips,PhyloSim-method	getNtips.PhyloSim
getNtips.PhyloSim	getNtips.PhyloSim
getOmegas	Undocumented.PhyloSim
getOmegas,CodonSequence-method	getOmegas.CodonSequence
getOmegas.CodonSequence	getOmegas.CodonSequence
getOmegas.Sequence	getOmegas.CodonSequence
getOmegaScalingFactor	Undocumented.PhyloSim
getOmegaScalingFactor,GY94-method	getOmegaScalingFactor.GY94
getOmegaScalingFactor.GY94	getOmegaScalingFactor.GY94
getParameterAtSite	Undocumented.PhyloSim
getParameterAtSite,Process-method	getParameterAtSite.Process
getParameterAtSite.Process	getParameterAtSite.Process
getParameterAtSites	Undocumented.PhyloSim
getParameterAtSites,Sequence-method	getParameterAtSites.Sequence
getParameterAtSites.Sequence	getParameterAtSites.Sequence
getPhylo	Undocumented.PhyloSim
getPhylo,PhyloSim-method	getPhylo.PhyloSim
getPhylo.PhyloSim	getPhylo.PhyloSim
getPosition,Event-method	getPosition.Event
getPosition.Event	getPosition.Event
getProbs	Undocumented.PhyloSim
getProbs,DiscreteDeletor-method	getProbs.DiscreteDeletor
getProbs,DiscreteInsertor-method	getProbs.DiscreteInsertor
getProbs.DiscreteDeletor	getProbs.DiscreteDeletor
getProbs.DiscreteInsertor	getProbs.DiscreteInsertor
getProcess	Undocumented.PhyloSim
getProcess,Event-method	getProcess.Event
getProcess,QMatrix-method	getProcess.QMatrix
getProcess.Event	getProcess.Event
getProcess.QMatrix	getProcess.QMatrix
getProcesses	Undocumented.PhyloSim
getProcesses,Sequence-method	getProcesses.Sequence
getProcesses,Site-method	getProcesses.Site
getProcesses.Sequence	getProcesses.Sequence
getProcesses.Site	getProcesses.Site
getProposeBy	Undocumented.PhyloSim
getProposeBy,GeneralInDel-method	getProposeBy.GeneralInDel
getProposeBy.GeneralInDel	getProposeBy.GeneralInDel
getProposeBy.GeneralInsertor	getProposeBy.GeneralInDel
getQMatrix	Undocumented.PhyloSim
getQMatrix,GeneralSubstitution-method	getQMatrix.GeneralSubstitution
getQMatrix,ToleranceSubstitution-method	getQMatrix.ToleranceSubstitution
getQMatrix.GeneralSubstitution	getQMatrix.GeneralSubstitution
getQMatrix.ToleranceSubstitution	getQMatrix.ToleranceSubstitution
getRate	Undocumented.PhyloSim
getRate,Event-method	getRate.Event
getRate,GeneralInDel-method	getRate.GeneralInDel
getRate,GeneralSubstitution-method	getRate.GeneralSubstitution
getRate,QMatrix-method	getRate.QMatrix
getRate,ToleranceSubstitution-method	getRate.ToleranceSubstitution
getRate.Event	getRate.Event
getRate.GeneralInDel	getRate.GeneralInDel
getRate.GeneralSubstitution	getRate.GeneralSubstitution
getRate.QMatrix	getRate.QMatrix
getRate.ToleranceSubstitution	getRate.ToleranceSubstitution
getRateList	Undocumented.PhyloSim
getRateList,GeneralSubstitution-method	getRateList.GeneralSubstitution
getRateList,QMatrix-method	getRateList.QMatrix
getRateList,ToleranceSubstitution-method	getRateList.ToleranceSubstitution
getRateList.GeneralSubstitution	getRateList.GeneralSubstitution
getRateList.QMatrix	getRateList.QMatrix
getRateList.ToleranceSubstitution	getRateList.ToleranceSubstitution
getRateMultipliers	Undocumented.PhyloSim
getRateMultipliers,Sequence-method	getRateMultipliers.Sequence
getRateMultipliers.Sequence	getRateMultipliers.Sequence
getRateParam	Undocumented.PhyloSim
getRateParam,F81-method	getRateParam.F81
getRateParam,F84-method	getRateParam.F84
getRateParam,GTR-method	getRateParam.GTR
getRateParam,HKY-method	getRateParam.HKY
getRateParam,K80-method	getRateParam.K80
getRateParam,K81-method	getRateParam.K81
getRateParam,T92-method	getRateParam.T92
getRateParam,TN93-method	getRateParam.TN93
getRateParam.F81	getRateParam.F81
getRateParam.F84	getRateParam.F84
getRateParam.GTR	getRateParam.GTR
getRateParam.HKY	getRateParam.HKY
getRateParam.K80	getRateParam.K80
getRateParam.K81	getRateParam.K81
getRateParam.T92	getRateParam.T92
getRateParam.TN93	getRateParam.TN93
getRateParamList	Undocumented.PhyloSim
getRateParamList,F81-method	getRateParamList.F81
getRateParamList,F84-method	getRateParamList.F84
getRateParamList,GTR-method	getRateParamList.GTR
getRateParamList,HKY-method	getRateParamList.HKY
getRateParamList,K80-method	getRateParamList.K80
getRateParamList,K81-method	getRateParamList.K81
getRateParamList,T92-method	getRateParamList.T92
getRateParamList,TN93-method	getRateParamList.TN93
getRateParamList.F81	getRateParamList.F81
getRateParamList.F84	getRateParamList.F84
getRateParamList.GTR	getRateParamList.GTR
getRateParamList.HKY	getRateParamList.HKY
getRateParamList.K80	getRateParamList.K80
getRateParamList.K81	getRateParamList.K81
getRateParamList.T92	getRateParamList.T92
getRateParamList.TN93	getRateParamList.TN93
getRootNode	Undocumented.PhyloSim
getRootNode,PhyloSim-method	getRootNode.PhyloSim
getRootNode.PhyloSim	getRootNode.PhyloSim
getRootSeq	Undocumented.PhyloSim
getRootSeq,PhyloSim-method	getRootSeq.PhyloSim
getRootSeq.PhyloSim	getRootSeq.PhyloSim
getScale	Undocumented.PhyloSim
getScale,BrownianInsertor-method	getScale.BrownianInsertor
getScale.BrownianInsertor	getScale.BrownianInsertor
getScaledMatrix	Undocumented.PhyloSim
getScaledMatrix,QMatrix-method	getScaledMatrix.QMatrix
getScaledMatrix.QMatrix	getScaledMatrix.QMatrix
getSeqFromNode	Undocumented.PhyloSim
getSeqFromNode,PhyloSim-method	getSeqFromNode.PhyloSim
getSeqFromNode.PhyloSim	getSeqFromNode.PhyloSim
getSequence	Undocumented.PhyloSim
getSequence,Site-method	getSequence.Site
getSequence.Site	getSequence.Site
getSequences	Undocumented.PhyloSim
getSequences,PhyloSim-method	getSequences.PhyloSim
getSequences.PhyloSim	getSequences.PhyloSim
getSite	Undocumented.PhyloSim
getSite,Event-method	getSite.Event
getSite.Event	getSite.Event
getSites	Undocumented.PhyloSim
getSites,Sequence-method	getSites.Sequence
getSites.Sequence	getSites.Sequence
getSiteSpecificParamIds	Undocumented.PhyloSim
getSiteSpecificParamIds,Process-method	getSiteSpecificParamIds.Process
getSiteSpecificParamIds.Process	getSiteSpecificParamIds.Process
getSiteSpecificParamList	Undocumented.PhyloSim
getSiteSpecificParamList,Process-method	getSiteSpecificParamList.Process
getSiteSpecificParamList.Process	getSiteSpecificParamList.Process
getSize	Undocumented.PhyloSim
getSize,Alphabet-method	getSize.Alphabet
getSize.Alphabet	getSize.Alphabet
getSizes	Undocumented.PhyloSim
getSizes,DiscreteDeletor-method	getSizes.DiscreteDeletor
getSizes,DiscreteInsertor-method	getSizes.DiscreteInsertor
getSizes.DiscreteDeletor	getSizes.DiscreteDeletor
getSizes.DiscreteInsertor	getSizes.DiscreteInsertor
getState	Undocumented.PhyloSim
getState,Site-method	getState.Site
getState.Site	getState.Site
getStates	Undocumented.PhyloSim
getStates,Sequence-method	getStates.Sequence
getStates.Sequence	getStates.Sequence
getString	Undocumented.PhyloSim
getString,Sequence-method	getString.Sequence
getString.Sequence	getString.Sequence
getSymbolFreqs	Undocumented.PhyloSim
getSymbolFreqs,Sequence-method	getSymbolFreqs.Sequence
getSymbolFreqs.Sequence	getSymbolFreqs.Sequence
getSymbolLength	Undocumented.PhyloSim
getSymbolLength,Alphabet-method	getSymbolLength.Alphabet
getSymbolLength.Alphabet	getSymbolLength.Alphabet
getSymbols	Undocumented.PhyloSim
getSymbols,Alphabet-method	getSymbols.Alphabet
getSymbols.Alphabet	getSymbols.Alphabet
getTableId	Undocumented.PhyloSim
getTableId,CodonAlphabet-method	getTableId.CodonAlphabet
getTableId.CodonAlphabet	getTableId.CodonAlphabet
getTargetState	Undocumented.PhyloSim
getTemplateSeq	Undocumented.PhyloSim
getTemplateSeq,GeneralInsertor-method	getTemplateSeq.GeneralInsertor
getTemplateSeq.GeneralInsertor	getTemplateSeq.GeneralInsertor
getTheta	Undocumented.PhyloSim
getTheta,T92-method	getTheta.T92
getTheta.T92	getTheta.T92
getTipLabels	Undocumented.PhyloSim
getTipLabels,PhyloSim-method	getTipLabels.PhyloSim
getTipLabels.PhyloSim	getTipLabels.PhyloSim
getTips	Undocumented.PhyloSim
getTips,PhyloSim-method	getTips.PhyloSim
getTips.PhyloSim	getTips.PhyloSim
getToleranceMargin	Undocumented.PhyloSim
getToleranceMargin,FastFieldDeletor-method	getToleranceMargin.FastFieldDeletor
getToleranceMargin.FastFieldDeletor	getToleranceMargin.FastFieldDeletor
getTotalRate	Undocumented.PhyloSim
getTotalRate,Site-method	getTotalRate.Site
getTotalRate.Site	getTotalRate.Site
getTotalRates	Undocumented.PhyloSim
getTotalRates,Sequence-method	getTotalRates.Sequence
getTotalRates.Sequence	getTotalRates.Sequence
getTotalRatesFromRange	Undocumented.PhyloSim
getTotalRatesFromRange,Sequence-method	getTotalRatesFromRange.Sequence
getTotalRatesFromRange.Sequence	getTotalRatesFromRange.Sequence
getTransTable	Undocumented.PhyloSim
getTransTable,CodonAlphabet-method	getTransTable.CodonAlphabet
getTransTable.CodonAlphabet	getTransTable.CodonAlphabet
getTreeLength	Undocumented.PhyloSim
getTreeLength,PhyloSim-method	getTreeLength.PhyloSim
getTreeLength.PhyloSim	getTreeLength.PhyloSim
getType	Undocumented.PhyloSim
getType,Alphabet-method	getType.Alphabet
getType,BrownianInsertor-method	getType.BrownianInsertor
getType,FastFieldDeletor-method	getType.FastFieldDeletor
getType.Alphabet	getType.Alphabet
getType.BrownianInsertor	getType.BrownianInsertor
getType.FastFieldDeletor	getType.FastFieldDeletor
getUniqueAlphabets	Undocumented.PhyloSim
getUniqueAlphabets,Sequence-method	getUniqueAlphabets.Sequence
getUniqueAlphabets.Sequence	getUniqueAlphabets.Sequence
getUniqueProcesses	Undocumented.PhyloSim
getUniqueProcesses,Sequence-method	getUniqueProcesses.Sequence
getUniqueProcesses.Sequence	getUniqueProcesses.Sequence
getWriteProtected	Undocumented.PhyloSim
getWriteProtected,Alphabet-method	getWriteProtected.Alphabet
getWriteProtected,Event-method	getWriteProtected.Event
getWriteProtected,Process-method	getWriteProtected.Process
getWriteProtected,QMatrix-method	getWriteProtected.QMatrix
getWriteProtected,Sequence-method	getWriteProtected.Sequence
getWriteProtected.Alphabet	getWriteProtected.Alphabet
getWriteProtected.Event	getWriteProtected.Event
getWriteProtected.Process	getWriteProtected.Process
getWriteProtected.QMatrix	getWriteProtected.QMatrix
getWriteProtected.Sequence	getWriteProtected.Sequence
globalConsistencyCheck	Undocumented.PhyloSim
globalConsistencyCheck,PSRoot-method	globalConsistencyCheck.PSRoot
globalConsistencyCheck.PSRoot	globalConsistencyCheck.PSRoot
GTR	GTR
GTR.checkConsistency	checkConsistency.GTR
GTR.getBaseFreqs	getBaseFreqs.GTR
GTR.getRateParam	getRateParam.GTR
GTR.getRateParamList	getRateParamList.GTR
GTR.setBaseFreqs	setBaseFreqs.GTR
GTR.setRateParam	setRateParam.GTR
GTR.setRateParamList	setRateParamList.GTR
GTR.summary	summary.GTR
GY94	GY94
GY94.checkConsistency	checkConsistency.GY94
GY94.getCodonFreqs	getCodonFreqs.GY94
GY94.getEventsAtSite	getEventsAtSite.GY94
GY94.getKappa	getKappa.GY94
GY94.getOmegaScalingFactor	getOmegaScalingFactor.GY94
GY94.setCodonFreqs	setCodonFreqs.GY94
GY94.setKappa	setKappa.GY94
GY94.setRate	setRate.GY94
GY94.summary	summary.GY94
hasSiteSpecificParameter	Undocumented.PhyloSim
hasSiteSpecificParameter,Process-method	hasSiteSpecificParameter.Process
hasSiteSpecificParameter.Process	hasSiteSpecificParameter.Process
hasSymbols	Undocumented.PhyloSim
hasSymbols,Alphabet-method	hasSymbols.Alphabet
hasSymbols.Alphabet	hasSymbols.Alphabet
hasUndefinedRate	Undocumented.PhyloSim
hasUndefinedRate,GeneralInDel-method	hasUndefinedRate.GeneralInDel
hasUndefinedRate,GeneralSubstitution-method	hasUndefinedRate.GeneralSubstitution
hasUndefinedRate,Process-method	hasUndefinedRate.Process
hasUndefinedRate,ToleranceSubstitution-method	hasUndefinedRate.ToleranceSubstitution
hasUndefinedRate.GeneralInDel	hasUndefinedRate.GeneralInDel
hasUndefinedRate.GeneralSubstitution	hasUndefinedRate.GeneralSubstitution
hasUndefinedRate.Process	hasUndefinedRate.Process
hasUndefinedRate.ToleranceSubstitution	hasUndefinedRate.ToleranceSubstitution
HKY	HKY
HKY.checkConsistency	checkConsistency.HKY
HKY.getBaseFreqs	getBaseFreqs.HKY
HKY.getRateParam	getRateParam.HKY
HKY.getRateParamList	getRateParamList.HKY
HKY.setBaseFreqs	setBaseFreqs.HKY
HKY.setRateParam	setRateParam.HKY
HKY.setRateParamList	setRateParamList.HKY
HKY.summary	summary.HKY
insertSequence	Undocumented.PhyloSim
insertSequence,Sequence-method	insertSequence.Sequence
insertSequence.Sequence	insertSequence.Sequence
intersect	Undocumented.PhyloSim
intersect.list	Undocumented.PhyloSim
intersect.list,PSRoot-method	intersect.list.PSRoot
intersect.list.PSRoot	intersect.list.PSRoot
is	Undocumented.PhyloSim
is.Alphabet	is.Alphabet
is.Alphabet.default	is.Alphabet
is.CodonAlphabet	is.CodonAlphabet
is.CodonAlphabet.default	is.CodonAlphabet
is.CodonUNREST	is.CodonUNREST
is.CodonUNREST.default	is.CodonUNREST
is.Event	is.Event
is.Event.default	is.Event
is.GeneralDeletor	is.GeneralDeletor
is.GeneralDeletor.default	is.GeneralDeletor
is.GeneralInDel	is.GeneralInDel
is.GeneralInDel.default	is.GeneralInDel
is.GeneralInsertor	is.GeneralInsertor
is.GeneralInsertor.default	is.GeneralInsertor
is.GeneralSubstitution	is.GeneralSubstitution
is.GeneralSubstitution.default	is.GeneralSubstitution
is.GY94	is.GY94
is.GY94.default	is.GY94
is.na,PSRoot-method	is.na.PSRoot
is.na.PSRoot	is.na.PSRoot
is.phylo	is.phylo
is.phylo.default	is.phylo
is.Process	is.Process
is.Process.default	is.Process
is.PSRoot	is.PSRoot
is.PSRoot.default	is.PSRoot
is.QMatrix	is.QMatrix
is.QMatrix.default	is.QMatrix
is.Sequence	is.Sequence
is.Sequence.default	is.Sequence
is.Site	is.Site
is.Site.default	is.Site
is.tip	Undocumented.PhyloSim
is.tip,PhyloSim-method	is.tip.PhyloSim
is.tip.PhyloSim	is.tip.PhyloSim
is.ToleranceSubstitution	is.ToleranceSubstitution
is.ToleranceSubstitution.default	is.ToleranceSubstitution
isAttached	Undocumented.PhyloSim
isAttached,Site-method	isAttached.Site
isAttached.Site	isAttached.Site
isEmpty	Undocumented.PhyloSim
isEmpty,Alphabet-method	isEmpty.Alphabet
isEmpty.Alphabet	isEmpty.Alphabet
isStartCodon	Undocumented.PhyloSim
isStartCodon,CodonAlphabet-method	isStartCodon.CodonAlphabet
isStartCodon.CodonAlphabet	isStartCodon.CodonAlphabet
isStopCodon	Undocumented.PhyloSim
isStopCodon,CodonAlphabet-method	isStopCodon.CodonAlphabet
isStopCodon.CodonAlphabet	isStopCodon.CodonAlphabet
JC69	JC69
JC69.checkConsistency	checkConsistency.JC69
JC69.summary	summary.JC69
JTT	JTT
JTT.dcmut	JTT.dcmut
K80	K80
K80.checkConsistency	checkConsistency.K80
K80.getBaseFreqs	getBaseFreqs.K80
K80.getRateParam	getRateParam.K80
K80.getRateParamList	getRateParamList.K80
K80.setBaseFreqs	setBaseFreqs.K80
K80.setRateParam	setRateParam.K80
K80.setRateParamList	setRateParamList.K80
K80.summary	summary.K80
K81	K81
K81.checkConsistency	checkConsistency.K81
K81.getBaseFreqs	getBaseFreqs.K81
K81.getRateParam	getRateParam.K81
K81.getRateParamList	getRateParamList.K81
K81.setBaseFreqs	setBaseFreqs.K81
K81.setRateParam	setRateParam.K81
K81.setRateParamList	setRateParamList.K81
K81.summary	summary.K81
LG	LG
list	Undocumented.PhyloSim
ll,PSRoot-method	ll.PSRoot
ll.PSRoot	ll.PSRoot
Log	Undocumented.PhyloSim
Log,PhyloSim-method	Log.PhyloSim
Log.PhyloSim	Log.PhyloSim
mtArt	mtArt
mtMam	mtMam
mtREV24	mtREV24
MtZoa	MtZoa
my	Undocumented.PhyloSim
my.all.equal	Undocumented.PhyloSim
my.all.equal,PSRoot-method	my.all.equal.PSRoot
my.all.equal.PSRoot	my.all.equal.PSRoot
newAAMatrix	Undocumented.PhyloSim
newAAMatrix,AminoAcidSubst-method	newAAMatrix.AminoAcidSubst
newAAMatrix.AminoAcidSubst	newAAMatrix.AminoAcidSubst
newMatrix	Undocumented.PhyloSim
newMatrix,CodonSubst-method	newMatrix.CodonSubst
newMatrix.CodonSubst	newMatrix.CodonSubst
NucleotideAlphabet	NucleotideAlphabet
NucleotideSequence	NucleotideSequence
NucleotideSequence.revComp	revComp.NucleotideSequence
omegaHist	Undocumented.PhyloSim
omegaHist,CodonSequence-method	omegaHist.CodonSequence
omegaHist.CodonSequence	omegaHist.CodonSequence
omegaVarM0	Undocumented.PhyloSim
omegaVarM0,CodonSequence-method	omegaVarM0.CodonSequence
omegaVarM0.CodonSequence	omegaVarM0.CodonSequence
omegaVarM1	Undocumented.PhyloSim
omegaVarM1,CodonSequence-method	omegaVarM1.CodonSequence
omegaVarM1.CodonSequence	omegaVarM1.CodonSequence
omegaVarM10Cont	Undocumented.PhyloSim
omegaVarM2	Undocumented.PhyloSim
omegaVarM2,CodonSequence-method	omegaVarM2.CodonSequence
omegaVarM2.CodonSequence	omegaVarM2.CodonSequence
omegaVarM3	Undocumented.PhyloSim
omegaVarM3,CodonSequence-method	omegaVarM3.CodonSequence
omegaVarM3.CodonSequence	omegaVarM3.CodonSequence
omegaVarM4	Undocumented.PhyloSim
omegaVarM4,CodonSequence-method	omegaVarM4.CodonSequence
omegaVarM4.CodonSequence	omegaVarM4.CodonSequence
PAM	PAM
PAM.dcmut	PAM.dcmut
Perform	Undocumented.PhyloSim
Perform,Event-method	Perform.Event
Perform.Event	Perform.Event
PhyloSim	PhyloSim
phylosim	PhyloSim
PhyloSim.as.character	as.character.PhyloSim
PhyloSim.attachHookToNode	attachHookToNode.PhyloSim
PhyloSim.attachSeqToNode	attachSeqToNode.PhyloSim
PhyloSim.checkConsistency	checkConsistency.PhyloSim
PhyloSim.Debug	Debug.PhyloSim
PhyloSim.detachHookFromNode	detachHookFromNode.PhyloSim
PhyloSim.detachSeqFromNode	detachSeqFromNode.PhyloSim
PhyloSim.exportStatTree	exportStatTree.PhyloSim
PhyloSim.getAlignment	getAlignment.PhyloSim
PhyloSim.getAlignmentLength	getAlignmentLength.PhyloSim
PhyloSim.getBranchEvents	getBranchEvents.PhyloSim
PhyloSim.getEdge	getEdge.PhyloSim
PhyloSim.getEdges	getEdges.PhyloSim
PhyloSim.getId	getId.PhyloSim
PhyloSim.getLogFile	getLogFile.PhyloSim
PhyloSim.getLogLevel	getLogLevel.PhyloSim
PhyloSim.getName	getName.PhyloSim
PhyloSim.getNedges	getNedges.PhyloSim
PhyloSim.getNodes	getNodes.PhyloSim
PhyloSim.getNtips	getNtips.PhyloSim
PhyloSim.getPhylo	getPhylo.PhyloSim
PhyloSim.getRootNode	getRootNode.PhyloSim
PhyloSim.getRootSeq	getRootSeq.PhyloSim
PhyloSim.getSeqFromNode	getSeqFromNode.PhyloSim
PhyloSim.getSequences	getSequences.PhyloSim
PhyloSim.getTipLabels	getTipLabels.PhyloSim
PhyloSim.getTips	getTips.PhyloSim
PhyloSim.getTreeLength	getTreeLength.PhyloSim
PhyloSim.is.tip	is.tip.PhyloSim
PhyloSim.Log	Log.PhyloSim
PhyloSim.plot	plot.PhyloSim
PhyloSim.readAlignment	readAlignment.PhyloSim
PhyloSim.readTree	readTree.PhyloSim
PhyloSim.saveAlignment	saveAlignment.PhyloSim
PhyloSim.scaleTree	scaleTree.PhyloSim
PhyloSim.setAlignment	setAlignment.PhyloSim
PhyloSim.setBranchEvents	setBranchEvents.PhyloSim
PhyloSim.setEdges	setEdges.PhyloSim
PhyloSim.setId	setId.PhyloSim
PhyloSim.setLogFile	setLogFile.PhyloSim
PhyloSim.setLogLevel	setLogLevel.PhyloSim
PhyloSim.setName	setName.PhyloSim
PhyloSim.setNedges	setNedges.PhyloSim
PhyloSim.setNodes	setNodes.PhyloSim
PhyloSim.setNtips	setNtips.PhyloSim
PhyloSim.setPhylo	setPhylo.PhyloSim
PhyloSim.setRootNode	setRootNode.PhyloSim
PhyloSim.setRootSeq	setRootSeq.PhyloSim
PhyloSim.setSequences	setSequences.PhyloSim
PhyloSim.setTipLabels	setTipLabels.PhyloSim
PhyloSim.setTips	setTips.PhyloSim
PhyloSim.setTreeLength	setTreeLength.PhyloSim
PhyloSim.Simulate	Simulate.PhyloSim
PhyloSim.summary	summary.PhyloSim
PhyloSim.Undocumented	Undocumented.PhyloSim
plot	Undocumented.PhyloSim
plot,ContinuousDeletor-method	plot.ContinuousDeletor
plot,ContinuousInsertor-method	plot.ContinuousInsertor
plot,DiscreteDeletor-method	plot.DiscreteDeletor
plot,DiscreteInsertor-method	plot.DiscreteInsertor
plot,GeneralSubstitution-method	plot.GeneralSubstitution
plot,PhyloSim-method	plot.PhyloSim
plot,Sequence-method	plot.Sequence
plot,ToleranceSubstitution-method	plot.ToleranceSubstitution
plot.ContinuousDeletor	plot.ContinuousDeletor
plot.ContinuousInsertor	plot.ContinuousInsertor
plot.DiscreteDeletor	plot.DiscreteDeletor
plot.DiscreteInsertor	plot.DiscreteInsertor
plot.GeneralSubstitution	plot.GeneralSubstitution
plot.PhyloSim	plot.PhyloSim
plot.PSRoot	Undocumented.PhyloSim
plot.Sequence	plot.Sequence
plot.ToleranceSubstitution	plot.ToleranceSubstitution
plotParametersAtSites	Undocumented.PhyloSim
plotParametersAtSites,Sequence-method	plotParametersAtSites.Sequence
plotParametersAtSites.Sequence	plotParametersAtSites.Sequence
plusGamma	Undocumented.PhyloSim
plusGamma,Sequence-method	plusGamma.Sequence
plusGamma.Sequence	plusGamma.Sequence
plusInvGamma	Undocumented.PhyloSim
plusInvGamma,Sequence-method	plusInvGamma.Sequence
plusInvGamma.Sequence	plusInvGamma.Sequence
print,PSRootSummary-method	print.PSRootSummary
print,QMatrix-method	print.QMatrix
print.PSRootSummary	print.PSRootSummary
print.QMatrix	print.QMatrix
Process	Process
Process.==	000==.Process
Process.as.character	as.character.Process
Process.checkConsistency	checkConsistency.Process
Process.clone	clone.Process
Process.getAlphabet	getAlphabet.Process
Process.getEventsAtSite	getEventsAtSite.Process
Process.getId	getId.Process
Process.getName	getName.Process
Process.getParameterAtSite	getParameterAtSite.Process
Process.getSiteSpecificParamIds	getSiteSpecificParamIds.Process
Process.getSiteSpecificParamList	getSiteSpecificParamList.Process
Process.getWriteProtected	getWriteProtected.Process
Process.hasSiteSpecificParameter	hasSiteSpecificParameter.Process
Process.hasUndefinedRate	hasUndefinedRate.Process
Process.setAlphabet	setAlphabet.Process
Process.setId	setId.Process
Process.setName	setName.Process
Process.setParameterAtSite	setParameterAtSite.Process
Process.setSiteSpecificParamIds	setSiteSpecificParamIds.Process
Process.setSiteSpecificParamList	setSiteSpecificParamList.Process
Process.setWriteProtected	setWriteProtected.Process
Process.summary	summary.Process
proposeLength	Undocumented.PhyloSim
proposeLength,GeneralInDel-method	proposeLength.GeneralInDel
proposeLength.GeneralInDel	proposeLength.GeneralInDel
PSRoot	PSRoot
PSRoot.checkConsistency	checkConsistency.PSRoot
PSRoot.enableVirtual	enableVirtual.PSRoot
PSRoot.getComments	getComments.PSRoot
PSRoot.getMethodsList	getMethodsList.PSRoot
PSRoot.globalConsistencyCheck	globalConsistencyCheck.PSRoot
PSRoot.intersect.list	intersect.list.PSRoot
PSRoot.is.na	is.na.PSRoot
PSRoot.ll	ll.PSRoot
PSRoot.my.all.equal	my.all.equal.PSRoot
PSRoot.setComments	setComments.PSRoot
PSRoot.setMethodsList	setMethodsList.PSRoot
PSRoot.summary	summary.PSRoot
PSRoot.virtualAssignmentForbidden	virtualAssignmentForbidden.PSRoot
PSRootSummary	PSRootSummary
PSRootSummary.checkConsistency	checkConsistency.PSRootSummary
PSRootSummary.print	print.PSRootSummary
QMatrix	QMatrix
QMatrix.as.character	as.character.QMatrix
QMatrix.checkConsistency	checkConsistency.QMatrix
QMatrix.getAlphabet	getAlphabet.QMatrix
QMatrix.getEventRate	getEventRate.QMatrix
QMatrix.getId	getId.QMatrix
QMatrix.getMatrix	getMatrix.QMatrix
QMatrix.getName	getName.QMatrix
QMatrix.getProcess	getProcess.QMatrix
QMatrix.getRate	getRate.QMatrix
QMatrix.getRateList	getRateList.QMatrix
QMatrix.getScaledMatrix	getScaledMatrix.QMatrix
QMatrix.getWriteProtected	getWriteProtected.QMatrix
QMatrix.print	print.QMatrix
QMatrix.Scale	Scale.QMatrix
QMatrix.setAlphabet	setAlphabet.QMatrix
QMatrix.setId	setId.QMatrix
QMatrix.setMatrix	setMatrix.QMatrix
QMatrix.setName	setName.QMatrix
QMatrix.setProcess	setProcess.QMatrix
QMatrix.setRate	setRate.QMatrix
QMatrix.setRateList	setRateList.QMatrix
QMatrix.setScaledMatrix	setScaledMatrix.QMatrix
QMatrix.setWriteProtected	setWriteProtected.QMatrix
QMatrix.summary	summary.QMatrix
readAlignment	Undocumented.PhyloSim
readAlignment,PhyloSim-method	readAlignment.PhyloSim
readAlignment.PhyloSim	readAlignment.PhyloSim
readTree	Undocumented.PhyloSim
readTree,PhyloSim-method	readTree.PhyloSim
readTree.PhyloSim	readTree.PhyloSim
rescaleQMatrix	Undocumented.PhyloSim
rescaleQMatrix,GeneralSubstitution-method	rescaleQMatrix.GeneralSubstitution
rescaleQMatrix,ToleranceSubstitution-method	rescaleQMatrix.ToleranceSubstitution
rescaleQMatrix.GeneralSubstitution	rescaleQMatrix.GeneralSubstitution
rescaleQMatrix.ToleranceSubstitution	rescaleQMatrix.ToleranceSubstitution
revComp	Undocumented.PhyloSim
revComp,NucleotideSequence-method	revComp.NucleotideSequence
revComp.NucleotideSequence	revComp.NucleotideSequence
sampleState	Undocumented.PhyloSim
sampleState,GeneralSubstitution-method	sampleState.GeneralSubstitution
sampleState,ToleranceSubstitution-method	sampleState.ToleranceSubstitution
sampleState.GeneralSubstitution	sampleState.GeneralSubstitution
sampleState.ToleranceSubstitution	sampleState.ToleranceSubstitution
sampleStates	Undocumented.PhyloSim
sampleStates,Sequence-method	sampleStates.Sequence
sampleStates.Sequence	sampleStates.Sequence
saveAlignment	Undocumented.PhyloSim
saveAlignment,PhyloSim-method	saveAlignment.PhyloSim
saveAlignment.PhyloSim	saveAlignment.PhyloSim
saveLoadReference	Undocumented.PhyloSim
Scale	Undocumented.PhyloSim
Scale,QMatrix-method	Scale.QMatrix
Scale.QMatrix	Scale.QMatrix
scaleTree	Undocumented.PhyloSim
scaleTree,PhyloSim-method	scaleTree.PhyloSim
scaleTree.PhyloSim	scaleTree.PhyloSim
Sequence	Sequence
Sequence.as.character	as.character.Sequence
Sequence.attachProcess	attachProcess.Sequence
Sequence.checkConsistency	checkConsistency.Sequence
Sequence.clearStates	clearStates.Sequence
Sequence.clone	clone.Sequence
Sequence.copySubSequence	copySubSequence.Sequence
Sequence.deleteSubSequence	deleteSubSequence.Sequence
Sequence.detachProcess	detachProcess.Sequence
Sequence.getAlphabets	getAlphabets.Sequence
Sequence.getAncestral	getAncestral.Sequence
Sequence.getBigRate	getBigRate.Sequence
Sequence.getCumulativeRates	getCumulativeRates.Sequence
Sequence.getCumulativeRatesFromRange	getCumulativeRatesFromRange.Sequence
Sequence.getDeletionTolerance	getDeletionTolerance.Sequence
Sequence.getEvents	getEvents.Sequence
Sequence.getId	getId.Sequence
Sequence.getInsertionTolerance	getInsertionTolerance.Sequence
Sequence.getLength	getLength.Sequence
Sequence.getName	getName.Sequence
Sequence.getParameterAtSites	getParameterAtSites.Sequence
Sequence.getProcesses	getProcesses.Sequence
Sequence.getRateMultipliers	getRateMultipliers.Sequence
Sequence.getSites	getSites.Sequence
Sequence.getStates	getStates.Sequence
Sequence.getString	getString.Sequence
Sequence.getSymbolFreqs	getSymbolFreqs.Sequence
Sequence.getTotalRates	getTotalRates.Sequence
Sequence.getTotalRatesFromRange	getTotalRatesFromRange.Sequence
Sequence.getUniqueAlphabets	getUniqueAlphabets.Sequence
Sequence.getUniqueProcesses	getUniqueProcesses.Sequence
Sequence.getWriteProtected	getWriteProtected.Sequence
Sequence.insertSequence	insertSequence.Sequence
Sequence.plot	plot.Sequence
Sequence.plotParametersAtSites	plotParametersAtSites.Sequence
Sequence.plusGamma	plusGamma.Sequence
Sequence.plusInvGamma	plusInvGamma.Sequence
Sequence.sampleStates	sampleStates.Sequence
Sequence.setAlphabets	setAlphabets.Sequence
Sequence.setAncestral	setAncestral.Sequence
Sequence.setBigRate	setBigRate.Sequence
Sequence.setCumulativeRates	setCumulativeRates.Sequence
Sequence.setDeletionTolerance	setDeletionTolerance.Sequence
Sequence.setId	setId.Sequence
Sequence.setInsertionTolerance	setInsertionTolerance.Sequence
Sequence.setLength	setLength.Sequence
Sequence.setName	setName.Sequence
Sequence.setParameterAtSites	setParameterAtSites.Sequence
Sequence.setProcesses	setProcesses.Sequence
Sequence.setRateMultipliers	setRateMultipliers.Sequence
Sequence.setStates	setStates.Sequence
Sequence.setString	setString.Sequence
Sequence.setTotalRates	setTotalRates.Sequence
Sequence.setUniqueAlphabets	setUniqueAlphabets.Sequence
Sequence.setUniqueProcesses	setUniqueProcesses.Sequence
Sequence.setWriteProtected	setWriteProtected.Sequence
Sequence.summary	summary.Sequence
setAcceptBy	Undocumented.PhyloSim
setAcceptBy,GeneralInDel-method	setAcceptBy.GeneralInDel
setAcceptBy.GeneralInDel	setAcceptBy.GeneralInDel
setAcceptBy.GeneralInsertor	setAcceptBy.GeneralInDel
setAcceptWin	Undocumented.PhyloSim
setAcceptWin,GeneralInsertor-method	setAcceptWin.GeneralInsertor
setAcceptWin.GeneralInsertor	setAcceptWin.GeneralInsertor
setAlignment	Undocumented.PhyloSim
setAlignment,PhyloSim-method	setAlignment.PhyloSim
setAlignment.PhyloSim	setAlignment.PhyloSim
setAlphabet	Undocumented.PhyloSim
setAlphabet,GeneralSubstitution-method	setAlphabet.GeneralSubstitution
setAlphabet,Process-method	setAlphabet.Process
setAlphabet,QMatrix-method	setAlphabet.QMatrix
setAlphabet,Site-method	setAlphabet.Site
setAlphabet,ToleranceSubstitution-method	setAlphabet.ToleranceSubstitution
setAlphabet.GeneralSubstitution	setAlphabet.GeneralSubstitution
setAlphabet.Process	setAlphabet.Process
setAlphabet.QMatrix	setAlphabet.QMatrix
setAlphabet.Site	setAlphabet.Site
setAlphabet.ToleranceSubstitution	setAlphabet.ToleranceSubstitution
setAlphabets	Undocumented.PhyloSim
setAlphabets,Sequence-method	setAlphabets.Sequence
setAlphabets.Sequence	setAlphabets.Sequence
setAncestral	Undocumented.PhyloSim
setAncestral,Sequence-method	setAncestral.Sequence
setAncestral,Site-method	setAncestral.Site
setAncestral.Sequence	setAncestral.Sequence
setAncestral.Site	setAncestral.Site
setBaseFreqs	Undocumented.PhyloSim
setBaseFreqs,F81-method	setBaseFreqs.F81
setBaseFreqs,F84-method	setBaseFreqs.F84
setBaseFreqs,GTR-method	setBaseFreqs.GTR
setBaseFreqs,HKY-method	setBaseFreqs.HKY
setBaseFreqs,K80-method	setBaseFreqs.K80
setBaseFreqs,K81-method	setBaseFreqs.K81
setBaseFreqs,TN93-method	setBaseFreqs.TN93
setBaseFreqs.F81	setBaseFreqs.F81
setBaseFreqs.F84	setBaseFreqs.F84
setBaseFreqs.GTR	setBaseFreqs.GTR
setBaseFreqs.HKY	setBaseFreqs.HKY
setBaseFreqs.K80	setBaseFreqs.K80
setBaseFreqs.K81	setBaseFreqs.K81
setBaseFreqs.TN93	setBaseFreqs.TN93
setBigRate	Undocumented.PhyloSim
setBigRate,Sequence-method	setBigRate.Sequence
setBigRate.Sequence	setBigRate.Sequence
setBranchEvents	Undocumented.PhyloSim
setBranchEvents,PhyloSim-method	setBranchEvents.PhyloSim
setBranchEvents.PhyloSim	setBranchEvents.PhyloSim
setCodonFreqs	Undocumented.PhyloSim
setCodonFreqs,GY94-method	setCodonFreqs.GY94
setCodonFreqs.GY94	setCodonFreqs.GY94
setComments	Undocumented.PhyloSim
setComments,PSRoot-method	setComments.PSRoot
setComments.PSRoot	setComments.PSRoot
setCumulativeRates	Undocumented.PhyloSim
setCumulativeRates,Sequence-method	setCumulativeRates.Sequence
setCumulativeRates.Sequence	setCumulativeRates.Sequence
setDeletionTolerance	Undocumented.PhyloSim
setDeletionTolerance,Sequence-method	setDeletionTolerance.Sequence
setDeletionTolerance.Sequence	setDeletionTolerance.Sequence
setDist	Undocumented.PhyloSim
setDist,ContinuousDeletor-method	setDist.ContinuousDeletor
setDist,ContinuousInsertor-method	setDist.ContinuousInsertor
setDist.ContinuousDeletor	setDist.ContinuousDeletor
setDist.ContinuousInsertor	setDist.ContinuousInsertor
setEdges	Undocumented.PhyloSim
setEdges,PhyloSim-method	setEdges.PhyloSim
setEdges.PhyloSim	setEdges.PhyloSim
setEquDist	Undocumented.PhyloSim
setEquDist,GeneralSubstitution-method	setEquDist.GeneralSubstitution
setEquDist,ToleranceSubstitution-method	setEquDist.ToleranceSubstitution
setEquDist.AminoAcidSubst	setEquDist.GeneralSubstitution
setEquDist.CodonSubst	Undocumented.PhyloSim
setEquDist.GeneralSubstitution	setEquDist.GeneralSubstitution
setEquDist.ToleranceSubstitution	setEquDist.ToleranceSubstitution
setEvents	Undocumented.PhyloSim
setEvents,Site-method	setEvents.Site
setEvents.Site	setEvents.Site
setGenerateBy	Undocumented.PhyloSim
setGenerateBy,GeneralInsertor-method	setGenerateBy.GeneralInsertor
setGenerateBy.GeneralInsertor	setGenerateBy.GeneralInsertor
setHandler	Undocumented.PhyloSim
setHandler,Event-method	setHandler.Event
setHandler.Event	setHandler.Event
setId	Undocumented.PhyloSim
setId,PhyloSim-method	setId.PhyloSim
setId,Process-method	setId.Process
setId,QMatrix-method	setId.QMatrix
setId,Sequence-method	setId.Sequence
setId.PhyloSim	setId.PhyloSim
setId.Process	setId.Process
setId.QMatrix	setId.QMatrix
setId.Sequence	setId.Sequence
setInsertHook	Undocumented.PhyloSim
setInsertHook,GeneralInsertor-method	setInsertHook.GeneralInsertor
setInsertHook.GeneralInsertor	setInsertHook.GeneralInsertor
setInsertionTolerance	Undocumented.PhyloSim
setInsertionTolerance,Sequence-method	setInsertionTolerance.Sequence
setInsertionTolerance.Sequence	setInsertionTolerance.Sequence
setKappa	Undocumented.PhyloSim
setKappa,F84-method	setKappa.F84
setKappa,GY94-method	setKappa.GY94
setKappa.F84	setKappa.F84
setKappa.GY94	setKappa.GY94
setLength	Undocumented.PhyloSim
setLength,Sequence-method	setLength.Sequence
setLength.Sequence	setLength.Sequence
setLengthParam1	Undocumented.PhyloSim
setLengthParam1,FastFieldDeletor-method	setLengthParam1.FastFieldDeletor
setLengthParam1.FastFieldDeletor	setLengthParam1.FastFieldDeletor
setLengthParam2	Undocumented.PhyloSim
setLengthParam2,FastFieldDeletor-method	setLengthParam2.FastFieldDeletor
setLengthParam2.FastFieldDeletor	setLengthParam2.FastFieldDeletor
setLogFile	Undocumented.PhyloSim
setLogFile,PhyloSim-method	setLogFile.PhyloSim
setLogFile.PhyloSim	setLogFile.PhyloSim
setLogLevel	Undocumented.PhyloSim
setLogLevel,PhyloSim-method	setLogLevel.PhyloSim
setLogLevel.PhyloSim	setLogLevel.PhyloSim
setMatrix	Undocumented.PhyloSim
setMatrix,QMatrix-method	setMatrix.QMatrix
setMatrix.QMatrix	setMatrix.QMatrix
setMaxLength	Undocumented.PhyloSim
setMaxLength,ContinuousDeletor-method	setMaxLength.ContinuousDeletor
setMaxLength,ContinuousInsertor-method	setMaxLength.ContinuousInsertor
setMaxLength.ContinuousDeletor	setMaxLength.ContinuousDeletor
setMaxLength.ContinuousInsertor	setMaxLength.ContinuousInsertor
setMethodsList	Undocumented.PhyloSim
setMethodsList,PSRoot-method	setMethodsList.PSRoot
setMethodsList.PSRoot	setMethodsList.PSRoot
setName	Undocumented.PhyloSim
setName,Event-method	setName.Event
setName,PhyloSim-method	setName.PhyloSim
setName,Process-method	setName.Process
setName,QMatrix-method	setName.QMatrix
setName,Sequence-method	setName.Sequence
setName.Event	setName.Event
setName.PhyloSim	setName.PhyloSim
setName.Process	setName.Process
setName.QMatrix	setName.QMatrix
setName.Sequence	setName.Sequence
setNedges	Undocumented.PhyloSim
setNedges,PhyloSim-method	setNedges.PhyloSim
setNedges.PhyloSim	setNedges.PhyloSim
setNodes	Undocumented.PhyloSim
setNodes,PhyloSim-method	setNodes.PhyloSim
setNodes.PhyloSim	setNodes.PhyloSim
setNtips	Undocumented.PhyloSim
setNtips,PhyloSim-method	setNtips.PhyloSim
setNtips.PhyloSim	setNtips.PhyloSim
setOmegas	Undocumented.PhyloSim
setOmegas,CodonSequence-method	setOmegas.CodonSequence
setOmegas.CodonSequence	setOmegas.CodonSequence
setOmegas.Sequence	setOmegas.CodonSequence
setParameterAtSite	Undocumented.PhyloSim
setParameterAtSite,Process-method	setParameterAtSite.Process
setParameterAtSite.FastFieldDeletor	setParameterAtSite.Process
setParameterAtSite.Process	setParameterAtSite.Process
setParameterAtSites	Undocumented.PhyloSim
setParameterAtSites,Sequence-method	setParameterAtSites.Sequence
setParameterAtSites.Sequence	setParameterAtSites.Sequence
setPhylo	Undocumented.PhyloSim
setPhylo,PhyloSim-method	setPhylo.PhyloSim
setPhylo.PhyloSim	setPhylo.PhyloSim
setPosition	Undocumented.PhyloSim
setPosition,Event-method	setPosition.Event
setPosition.Event	setPosition.Event
setProbs	Undocumented.PhyloSim
setProbs,DiscreteDeletor-method	setProbs.DiscreteDeletor
setProbs,DiscreteInsertor-method	setProbs.DiscreteInsertor
setProbs.DiscreteDeletor	setProbs.DiscreteDeletor
setProbs.DiscreteInsertor	setProbs.DiscreteInsertor
setProcess	Undocumented.PhyloSim
setProcess,Event-method	setProcess.Event
setProcess,QMatrix-method	setProcess.QMatrix
setProcess.Event	setProcess.Event
setProcess.QMatrix	setProcess.QMatrix
setProcesses	Undocumented.PhyloSim
setProcesses,Sequence-method	setProcesses.Sequence
setProcesses,Site-method	setProcesses.Site
setProcesses.Sequence	setProcesses.Sequence
setProcesses.Site	setProcesses.Site
setProposeBy	Undocumented.PhyloSim
setProposeBy,GeneralInDel-method	setProposeBy.GeneralInDel
setProposeBy.GeneralInDel	setProposeBy.GeneralInDel
setProposeBy.GeneralInsertor	setProposeBy.GeneralInDel
setQMatrix	Undocumented.PhyloSim
setQMatrix,GeneralSubstitution-method	setQMatrix.GeneralSubstitution
setQMatrix,ToleranceSubstitution-method	setQMatrix.ToleranceSubstitution
setQMatrix.GeneralSubstitution	setQMatrix.GeneralSubstitution
setQMatrix.ToleranceSubstitution	setQMatrix.ToleranceSubstitution
setRate	Undocumented.PhyloSim
setRate,Event-method	setRate.Event
setRate,GeneralInDel-method	setRate.GeneralInDel
setRate,GeneralSubstitution-method	setRate.GeneralSubstitution
setRate,GY94-method	setRate.GY94
setRate,QMatrix-method	setRate.QMatrix
setRate,ToleranceSubstitution-method	setRate.ToleranceSubstitution
setRate.Event	setRate.Event
setRate.GeneralInDel	setRate.GeneralInDel
setRate.GeneralSubstitution	setRate.GeneralSubstitution
setRate.GY94	setRate.GY94
setRate.QMatrix	setRate.QMatrix
setRate.ToleranceSubstitution	setRate.ToleranceSubstitution
setRateList	Undocumented.PhyloSim
setRateList,GeneralSubstitution-method	setRateList.GeneralSubstitution
setRateList,QMatrix-method	setRateList.QMatrix
setRateList,ToleranceSubstitution-method	setRateList.ToleranceSubstitution
setRateList.GeneralSubstitution	setRateList.GeneralSubstitution
setRateList.QMatrix	setRateList.QMatrix
setRateList.ToleranceSubstitution	setRateList.ToleranceSubstitution
setRateMultipliers	Undocumented.PhyloSim
setRateMultipliers,Sequence-method	setRateMultipliers.Sequence
setRateMultipliers.Sequence	setRateMultipliers.Sequence
setRateParam	Undocumented.PhyloSim
setRateParam,F81-method	setRateParam.F81
setRateParam,F84-method	setRateParam.F84
setRateParam,GTR-method	setRateParam.GTR
setRateParam,HKY-method	setRateParam.HKY
setRateParam,K80-method	setRateParam.K80
setRateParam,K81-method	setRateParam.K81
setRateParam,T92-method	setRateParam.T92
setRateParam,TN93-method	setRateParam.TN93
setRateParam.F81	setRateParam.F81
setRateParam.F84	setRateParam.F84
setRateParam.GTR	setRateParam.GTR
setRateParam.HKY	setRateParam.HKY
setRateParam.K80	setRateParam.K80
setRateParam.K81	setRateParam.K81
setRateParam.T92	setRateParam.T92
setRateParam.TN93	setRateParam.TN93
setRateParamList	Undocumented.PhyloSim
setRateParamList,F81-method	setRateParamList.F81
setRateParamList,F84-method	setRateParamList.F84
setRateParamList,GTR-method	setRateParamList.GTR
setRateParamList,HKY-method	setRateParamList.HKY
setRateParamList,K80-method	setRateParamList.K80
setRateParamList,K81-method	setRateParamList.K81
setRateParamList,T92-method	setRateParamList.T92
setRateParamList,TN93-method	setRateParamList.TN93
setRateParamList.F81	setRateParamList.F81
setRateParamList.F84	setRateParamList.F84
setRateParamList.GTR	setRateParamList.GTR
setRateParamList.HKY	setRateParamList.HKY
setRateParamList.K80	setRateParamList.K80
setRateParamList.K81	setRateParamList.K81
setRateParamList.T92	setRateParamList.T92
setRateParamList.TN93	setRateParamList.TN93
setRootNode	Undocumented.PhyloSim
setRootNode,PhyloSim-method	setRootNode.PhyloSim
setRootNode.PhyloSim	setRootNode.PhyloSim
setRootSeq	Undocumented.PhyloSim
setRootSeq,PhyloSim-method	setRootSeq.PhyloSim
setRootSeq.PhyloSim	setRootSeq.PhyloSim
setScale	Undocumented.PhyloSim
setScale,BrownianInsertor-method	setScale.BrownianInsertor
setScale.BrownianInsertor	setScale.BrownianInsertor
setScaledMatrix	Undocumented.PhyloSim
setScaledMatrix,QMatrix-method	setScaledMatrix.QMatrix
setScaledMatrix.QMatrix	setScaledMatrix.QMatrix
setSequence	Undocumented.PhyloSim
setSequence,Site-method	setSequence.Site
setSequence.Site	setSequence.Site
setSequences	Undocumented.PhyloSim
setSequences,PhyloSim-method	setSequences.PhyloSim
setSequences.PhyloSim	setSequences.PhyloSim
setSite	Undocumented.PhyloSim
setSite,Event-method	setSite.Event
setSite.Event	setSite.Event
setSiteSpecificParamIds	Undocumented.PhyloSim
setSiteSpecificParamIds,Process-method	setSiteSpecificParamIds.Process
setSiteSpecificParamIds.Process	setSiteSpecificParamIds.Process
setSiteSpecificParamList	Undocumented.PhyloSim
setSiteSpecificParamList,Process-method	setSiteSpecificParamList.Process
setSiteSpecificParamList.Process	setSiteSpecificParamList.Process
setSize	Undocumented.PhyloSim
setSize,Alphabet-method	setSize.Alphabet
setSize.Alphabet	setSize.Alphabet
setSizes	Undocumented.PhyloSim
setSizes,DiscreteDeletor-method	setSizes.DiscreteDeletor
setSizes,DiscreteInsertor-method	setSizes.DiscreteInsertor
setSizes.DiscreteDeletor	setSizes.DiscreteDeletor
setSizes.DiscreteInsertor	setSizes.DiscreteInsertor
setState	Undocumented.PhyloSim
setState,Site-method	setState.Site
setState.Site	setState.Site
setStates	Undocumented.PhyloSim
setStates,Sequence-method	setStates.Sequence
setStates.Sequence	setStates.Sequence
setString	Undocumented.PhyloSim
setString,Sequence-method	setString.Sequence
setString.Sequence	setString.Sequence
setSymbolLength	Undocumented.PhyloSim
setSymbolLength,Alphabet-method	setSymbolLength.Alphabet
setSymbolLength.Alphabet	setSymbolLength.Alphabet
setSymbols	Undocumented.PhyloSim
setSymbols,Alphabet-method	setSymbols.Alphabet
setSymbols.Alphabet	setSymbols.Alphabet
setTableId	Undocumented.PhyloSim
setTableId,CodonAlphabet-method	setTableId.CodonAlphabet
setTableId.CodonAlphabet	setTableId.CodonAlphabet
setTargetState	Undocumented.PhyloSim
setTemplateSeq	Undocumented.PhyloSim
setTemplateSeq,GeneralInsertor-method	setTemplateSeq.GeneralInsertor
setTemplateSeq.GeneralInsertor	setTemplateSeq.GeneralInsertor
setTheta	Undocumented.PhyloSim
setTheta,T92-method	setTheta.T92
setTheta.T92	setTheta.T92
setTipLabels	Undocumented.PhyloSim
setTipLabels,PhyloSim-method	setTipLabels.PhyloSim
setTipLabels.PhyloSim	setTipLabels.PhyloSim
setTips	Undocumented.PhyloSim
setTips,PhyloSim-method	setTips.PhyloSim
setTips.PhyloSim	setTips.PhyloSim
setToleranceMargin	Undocumented.PhyloSim
setToleranceMargin,FastFieldDeletor-method	setToleranceMargin.FastFieldDeletor
setToleranceMargin.FastFieldDeletor	setToleranceMargin.FastFieldDeletor
setTotalRate	Undocumented.PhyloSim
setTotalRate,Site-method	setTotalRate.Site
setTotalRate.Site	setTotalRate.Site
setTotalRates	Undocumented.PhyloSim
setTotalRates,Sequence-method	setTotalRates.Sequence
setTotalRates.Sequence	setTotalRates.Sequence
setTransTable	Undocumented.PhyloSim
setTransTable,CodonAlphabet-method	setTransTable.CodonAlphabet
setTransTable.CodonAlphabet	setTransTable.CodonAlphabet
setTreeLength	Undocumented.PhyloSim
setTreeLength,PhyloSim-method	setTreeLength.PhyloSim
setTreeLength.PhyloSim	setTreeLength.PhyloSim
setType	Undocumented.PhyloSim
setType,Alphabet-method	setType.Alphabet
setType,BrownianInsertor-method	setType.BrownianInsertor
setType,FastFieldDeletor-method	setType.FastFieldDeletor
setType.Alphabet	setType.Alphabet
setType.BrownianInsertor	setType.BrownianInsertor
setType.FastFieldDeletor	setType.FastFieldDeletor
setUniqueAlphabets	Undocumented.PhyloSim
setUniqueAlphabets,Sequence-method	setUniqueAlphabets.Sequence
setUniqueAlphabets.Sequence	setUniqueAlphabets.Sequence
setUniqueProcesses	Undocumented.PhyloSim
setUniqueProcesses,Sequence-method	setUniqueProcesses.Sequence
setUniqueProcesses.Sequence	setUniqueProcesses.Sequence
setWriteProtected	Undocumented.PhyloSim
setWriteProtected,Alphabet-method	setWriteProtected.Alphabet
setWriteProtected,Event-method	setWriteProtected.Event
setWriteProtected,Process-method	setWriteProtected.Process
setWriteProtected,QMatrix-method	setWriteProtected.QMatrix
setWriteProtected,Sequence-method	setWriteProtected.Sequence
setWriteProtected.Alphabet	setWriteProtected.Alphabet
setWriteProtected.Event	setWriteProtected.Event
setWriteProtected.Process	setWriteProtected.Process
setWriteProtected.QMatrix	setWriteProtected.QMatrix
setWriteProtected.Sequence	setWriteProtected.Sequence
Simulate	Undocumented.PhyloSim
Simulate,PhyloSim-method	Simulate.PhyloSim
Simulate.PhyloSim	Simulate.PhyloSim
Site	Site
Site.as.character	as.character.Site
Site.attachProcess	attachProcess.Site
Site.checkConsistency	checkConsistency.Site
Site.detachProcess	detachProcess.Site
Site.flagTotalRate	flagTotalRate.Site
Site.getAlphabet	getAlphabet.Site
Site.getAncestral	getAncestral.Site
Site.getEvents	getEvents.Site
Site.getProcesses	getProcesses.Site
Site.getSequence	getSequence.Site
Site.getState	getState.Site
Site.getTotalRate	getTotalRate.Site
Site.isAttached	isAttached.Site
Site.setAlphabet	setAlphabet.Site
Site.setAncestral	setAncestral.Site
Site.setEvents	setEvents.Site
Site.setProcesses	setProcesses.Site
Site.setSequence	setSequence.Site
Site.setState	setState.Site
Site.setTotalRate	setTotalRate.Site
Site.summary	summary.Site
stringLength	stringLength
stringLength.default	stringLength
stringLengthVector	stringLengthVector
stringLengthVector.default	stringLengthVector
summary,Alphabet-method	summary.Alphabet
summary,AminoAcidSubst-method	summary.AminoAcidSubst
summary,BinarySubst-method	summary.BinarySubst
summary,BrownianInsertor-method	summary.BrownianInsertor
summary,CodonAlphabet-method	summary.CodonAlphabet
summary,CodonSubst-method	summary.CodonSubst
summary,ContinuousDeletor-method	summary.ContinuousDeletor
summary,ContinuousInsertor-method	summary.ContinuousInsertor
summary,DiscreteDeletor-method	summary.DiscreteDeletor
summary,DiscreteInsertor-method	summary.DiscreteInsertor
summary,Event-method	summary.Event
summary,F81-method	summary.F81
summary,F84-method	summary.F84
summary,FastFieldDeletor-method	summary.FastFieldDeletor
summary,GeneralDeletor-method	summary.GeneralDeletor
summary,GeneralInDel-method	summary.GeneralInDel
summary,GeneralInsertor-method	summary.GeneralInsertor
summary,GeneralSubstitution-method	summary.GeneralSubstitution
summary,GTR-method	summary.GTR
summary,GY94-method	summary.GY94
summary,HKY-method	summary.HKY
summary,JC69-method	summary.JC69
summary,K80-method	summary.K80
summary,K81-method	summary.K81
summary,PhyloSim-method	summary.PhyloSim
summary,Process-method	summary.Process
summary,PSRoot-method	summary.PSRoot
summary,QMatrix-method	summary.QMatrix
summary,Sequence-method	summary.Sequence
summary,Site-method	summary.Site
summary,T92-method	summary.T92
summary,TN93-method	summary.TN93
summary,ToleranceSubstitution-method	summary.ToleranceSubstitution
summary,UNREST-method	summary.UNREST
summary.Alphabet	summary.Alphabet
summary.AminoAcidSubst	summary.AminoAcidSubst
summary.BinarySubst	summary.BinarySubst
summary.BrownianInsertor	summary.BrownianInsertor
summary.CodonAlphabet	summary.CodonAlphabet
summary.CodonSubst	summary.CodonSubst
summary.ContinuousDeletor	summary.ContinuousDeletor
summary.ContinuousInsertor	summary.ContinuousInsertor
summary.DiscreteDeletor	summary.DiscreteDeletor
summary.DiscreteInsertor	summary.DiscreteInsertor
summary.Event	summary.Event
summary.F81	summary.F81
summary.F84	summary.F84
summary.FastFieldDeletor	summary.FastFieldDeletor
summary.GeneralDeletor	summary.GeneralDeletor
summary.GeneralInDel	summary.GeneralInDel
summary.GeneralInsertor	summary.GeneralInsertor
summary.GeneralSubstitution	summary.GeneralSubstitution
summary.GTR	summary.GTR
summary.GY94	summary.GY94
summary.HKY	summary.HKY
summary.JC69	summary.JC69
summary.K80	summary.K80
summary.K81	summary.K81
summary.PhyloSim	summary.PhyloSim
summary.Process	summary.Process
summary.PSRoot	summary.PSRoot
summary.QMatrix	summary.QMatrix
summary.Sequence	summary.Sequence
summary.Site	summary.Site
summary.T92	summary.T92
summary.TN93	summary.TN93
summary.ToleranceSubstitution	summary.ToleranceSubstitution
summary.UNREST	summary.UNREST
T92	T92
T92.checkConsistency	checkConsistency.T92
T92.getRateParam	getRateParam.T92
T92.getRateParamList	getRateParamList.T92
T92.getTheta	getTheta.T92
T92.setRateParam	setRateParam.T92
T92.setRateParamList	setRateParamList.T92
T92.setTheta	setTheta.T92
T92.summary	summary.T92
tip	Undocumented.PhyloSim
TN93	TN93
TN93.checkConsistency	checkConsistency.TN93
TN93.getBaseFreqs	getBaseFreqs.TN93
TN93.getRateParam	getRateParam.TN93
TN93.getRateParamList	getRateParamList.TN93
TN93.setBaseFreqs	setBaseFreqs.TN93
TN93.setRateParam	setRateParam.TN93
TN93.setRateParamList	setRateParamList.TN93
TN93.summary	summary.TN93
ToleranceSubstitution	ToleranceSubstitution
ToleranceSubstitution.as.character	as.character.ToleranceSubstitution
ToleranceSubstitution.checkConsistency	checkConsistency.ToleranceSubstitution
ToleranceSubstitution.clone	clone.ToleranceSubstitution
ToleranceSubstitution.getAlphabet	getAlphabet.ToleranceSubstitution
ToleranceSubstitution.getEquDist	getEquDist.ToleranceSubstitution
ToleranceSubstitution.getEventRate	getEventRate.ToleranceSubstitution
ToleranceSubstitution.getEventRateAtSite	getEventRateAtSite.ToleranceSubstitution
ToleranceSubstitution.getEventsAtSite	getEventsAtSite.ToleranceSubstitution
ToleranceSubstitution.getQMatrix	getQMatrix.ToleranceSubstitution
ToleranceSubstitution.getRate	getRate.ToleranceSubstitution
ToleranceSubstitution.getRateList	getRateList.ToleranceSubstitution
ToleranceSubstitution.hasUndefinedRate	hasUndefinedRate.ToleranceSubstitution
ToleranceSubstitution.plot	plot.ToleranceSubstitution
ToleranceSubstitution.rescaleQMatrix	rescaleQMatrix.ToleranceSubstitution
ToleranceSubstitution.sampleState	sampleState.ToleranceSubstitution
ToleranceSubstitution.setAlphabet	setAlphabet.ToleranceSubstitution
ToleranceSubstitution.setEquDist	setEquDist.ToleranceSubstitution
ToleranceSubstitution.setQMatrix	setQMatrix.ToleranceSubstitution
ToleranceSubstitution.setRate	setRate.ToleranceSubstitution
ToleranceSubstitution.setRateList	setRateList.ToleranceSubstitution
ToleranceSubstitution.summary	summary.ToleranceSubstitution
Translate	Undocumented.PhyloSim
Translate,CodonSequence-method	Translate.CodonSequence
Translate.CodonSequence	Translate.CodonSequence
translateCodon	Undocumented.PhyloSim
translateCodon,CodonAlphabet-method	translateCodon.CodonAlphabet
translateCodon.CodonAlphabet	translateCodon.CodonAlphabet
Undocumented	Undocumented.PhyloSim
Undocumented,PhyloSim-method	Undocumented.PhyloSim
Undocumented.PhyloSim	Undocumented.PhyloSim
UNREST	UNREST
UNREST.checkConsistency	checkConsistency.UNREST
UNREST.summary	summary.UNREST
virtualAssignmentForbidden	Undocumented.PhyloSim
virtualAssignmentForbidden,PSRoot-method	virtualAssignmentForbidden.PSRoot
virtualAssignmentForbidden.PSRoot	virtualAssignmentForbidden.PSRoot
WAG	WAG
