API for phylosim
Flexible Simulations of Biological Sequence Evolution

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