==.Alphabet             Check if two alaphabet objects have the same
                        symbol set
==.Process              Check whether the two supplied Process objects
                        are identical
Alphabet                The Alphabet class
AminoAcidAlphabet       The AminoAcidAlphabet class
AminoAcidSequence       The AminoAcidSequence class
AminoAcidSubst          The AminoAcidSubst class
AnyAlphabet             The AnyAlphabet class
BinaryAlphabet          The BinaryAlphabet class
BinarySequence          The BinarySequence class
BinarySubst             The BinarySubst class
BrownianInsertor        The BrownianInsertor class
BrownianPath.BrownianInsertor
                        Generate a Brownian path
CodonAlphabet           The CodonAlphabet class
CodonSequence           The CodonSequence class
CodonSubst              The CodonSubst class
CodonUNREST             The CodonUNREST class
ContinuousDeletor       The ContinuousDeletor class
ContinuousInsertor      The ContinuousInsertor class
Debug.PhyloSim          Save a debug message in the PhyloSim log file
DiscreteDeletor         The DiscreteDeletor class
DiscreteInsertor        The DiscreteInsertor class
ECMrest                 The ECMrest empirical codon substitution model
ECMunrest               The ECMunrest empirical codon substitution
                        model
Event                   The Event class
F81                     The F81 class
F84                     The F84 class
FastFieldDeletor        The FastFieldDeletor class
GTR                     The GTR class
GY94                    The GY94 class
GeneralDeletor          The GeneralDeletor class
GeneralInDel            The GeneralInDel class
GeneralInsertor         The GeneralInsertor class
GeneralSubstitution     The GeneralSubstitution class
HKY                     The HKY class
JC69                    The JC69 class
JTT                     The JTT empirical amino acid substitution model
JTT.dcmut               The JTT.dcmut empirical amino acid substitution
                        model
K80                     The K80 class
K81                     The K81 class
LG                      The LG empirical amino acid substitution model
Log.PhyloSim            Save a message in the PhyloSim log file
MtZoa                   The MtZoa empirical amino acid substitution
                        model
NucleotideAlphabet      The NucleotideAlphabet class
NucleotideSequence      The NucleotideSequence class
PAM                     The PAM empirical amino acid substitution model
PAM.dcmut               The PAM.dcmut empirical amino acid substitution
                        model
PSRoot                  The root class for all phylosim objects
PSRootSummary           The PSRootSummary class
Perform.Event           Perform an event
PhyloSim                The PhyloSim class
Process                 The Process class
QMatrix                 The QMatrix class
Scale.QMatrix           Scale the scaled rate matrix stored in a
                        QMatrix object by the provided factor
Sequence                The Sequence class
Simulate.PhyloSim       Run a simulation according to a PhyloSim object
Site                    The Site class
T92                     The T92 class
TN93                    The TN93 class
ToleranceSubstitution   The ToleranceSubstitution class
Translate.CodonSequence
                        Translate a CodonSequence object
UNREST                  The UNREST class
Undocumented.PhyloSim   Undocumented object (PhyloSim package)
WAG                     The WAG empirical amino acid substitution model
areSynonymous.CodonAlphabet
                        Check whether two codons are synonymous
as.character.Alphabet   Get the character representation of an Alphabet
                        object
as.character.Event      Get the character representation of an Event
                        object
as.character.GeneralSubstitution
                        Return the character representation of a
                        GeneralSubstitution object
as.character.PhyloSim   Return the character representation of a
                        PhyloSim object
as.character.Process    Get the character representation of a Process
                        object
as.character.QMatrix    Return the character representation of a
                        QMatrix object
as.character.Sequence   Get the string representation of a Sequence
                        object
as.character.Site       Get the character representation of a Site
                        object
as.character.ToleranceSubstitution
                        Return the character representation of a
                        ToleranceSubstitution object
attachHookToNode.PhyloSim
                        Attach a callback function to a given node of a
                        phylo object aggregated by a PhyloSim object
attachProcess.Sequence
                        Attach a Process object to a set of Site
                        objects aggregated by a Sequence object
attachProcess.Site      Attach a Process object to a Site object
attachSeqToNode.PhyloSim
                        Assotiate a Sequence object with a given node
                        of a phylo object aggregated by a PhyloSim
                        object
buildFromPAML.AminoAcidSubst
                        Build rate matrix from PAML file
buildFromPAML.CodonSubst
                        Build rate matrix from PAML file
checkConsistency.Alphabet
                        Check object consistency
checkConsistency.AminoAcidSubst
                        Check object consistency
checkConsistency.BinarySubst
                        Check object consistency
checkConsistency.BrownianInsertor
                        Check object consistency
checkConsistency.CodonAlphabet
                        Check object consistency
checkConsistency.CodonSequence
                        Check object consistency
checkConsistency.CodonSubst
                        Check object consistency
checkConsistency.CodonUNREST
                        Check object consistency
checkConsistency.ContinuousDeletor
                        Check object consistency
checkConsistency.ContinuousInsertor
                        Check object consistency
checkConsistency.DiscreteDeletor
                        Check object consistency
checkConsistency.DiscreteInsertor
                        Check object consistency
checkConsistency.Event
                        Check object consistency
checkConsistency.F81    Check object consistency
checkConsistency.F84    Check object consistency
checkConsistency.FastFieldDeletor
                        Check object consistency
checkConsistency.GTR    Check object consistency
checkConsistency.GY94   Check object consistency
checkConsistency.GeneralDeletor
                        Check object consistency
checkConsistency.GeneralInDel
                        Check object consistency
checkConsistency.GeneralInsertor
                        Check object consistency
checkConsistency.GeneralSubstitution
                        Check object consistency
checkConsistency.HKY    Check object consistency
checkConsistency.JC69   Check object consistency
checkConsistency.K80    Check object consistency
checkConsistency.K81    Check object consistency
checkConsistency.PSRoot
                        Check object consistency
checkConsistency.PSRootSummary
                        Check object consistency
checkConsistency.PhyloSim
                        Check object consistency
checkConsistency.Process
                        Check object consistency
checkConsistency.QMatrix
                        Check object consistency
checkConsistency.Sequence
                        Check object consistency
checkConsistency.Site   Check object consistency
checkConsistency.T92    Check object consistency
checkConsistency.TN93   Check object consistency
checkConsistency.ToleranceSubstitution
                        Check object consistency
checkConsistency.UNREST
                        Check object consistency
clearStates.Sequence    Set the states of a collection of Site objects
                        aggregated by a Sequence object to undefined
                        (NA)
clone.GeneralSubstitution
                        Clone a GeneralSubstitution object
clone.Process           Clone a process object
clone.Sequence          Clone a Sequence object
clone.ToleranceSubstitution
                        Clone a ToleranceSubstitution object
copySubSequence.Sequence
                        Copy a collection of Site objects aggregated by
                        a Sequence object into a new Sequence object
cpREV                   The cpREV empirical amino acid substitution
                        model
deleteSubSequence.Sequence
                        Delete a collection of sites aggregated by a
                        Sequence object
detachHookFromNode.PhyloSim
                        Detach a node hook function from a given node
                        of a phylo object aggregated by a PhyloSim
                        object
detachProcess.Sequence
                        Detach a Process object from a set of Site
                        objects aggregated by a Sequence object
detachProcess.Site      Site
detachSeqFromNode.PhyloSim
                        Detach a Sequence object from a given node of a
                        phylo object aggregated by a PhyloSim object
enableVirtual.PSRoot    Enable the use of virtual fields for a given
                        object
exportStatTree.PhyloSim
                        Export the per-branch counts of an event as a
                        phylo object
flagTotalRate.Site      Flag the total event rate
generateInsert.GeneralInsertor
                        Generate an insert
getAcceptBy.GeneralInDel
                        Get the function used for accepting/rejecting
                        indel events
getAcceptWin.GeneralInsertor
                        Get the size of the acceptance window
getAlignment.PhyloSim   Get the alignment stored in a PhyloSim object
getAlignmentLength.PhyloSim
                        Get the alignment length from a PhyloSim object
getAlphabet.GeneralSubstitution
                        Get the Alphabet object aggregated by a
                        GeneralSubstitution object
getAlphabet.Process     Get the Alphabet object associated with a given
                        Process object
getAlphabet.QMatrix     Get the Alphabet object associated with a
                        QMatrix object
getAlphabet.Site        Get the Alphabet object attached to a Site
                        object
getAlphabet.ToleranceSubstitution
                        Get the Alphabet object aggregated by a
                        ToleranceSubstitution object
getAlphabets.Sequence   Get the list of the Alphabet objects attached
                        to the Site objects aggregated by a Sequence
                        object
getAncestral.Sequence   Get the ancestral object of a Sequence object
getAncestral.Site       Get the ancestral object of a Site object
getBaseFreqs.F81        Get the base frequency parameters
getBaseFreqs.F84        Get the base frequency parameters
getBaseFreqs.GTR        Get the base frequency parameters
getBaseFreqs.HKY        Get the base frequency parameters
getBaseFreqs.K80        Get the base frequency parameters
getBaseFreqs.K81        Get the base frequency parameters
getBaseFreqs.TN93       Get the base frequency parameters
getBigRate.Sequence     Get the sum of all active event rates from a
                        Sequence object
getBranchEvents.PhyloSim
                        Get the list of events having per-branch
                        statistics recorded
getCodonFreqs.GY94      Get codon frequencies
getComments.PSRoot      Get the comments associated with an object
getCumulativeRates.Sequence
                        Get the total site rates from a Sequence object
getCumulativeRatesFromRange.Sequence
                        Get the cumulative site rates for a collection
                        of Site objects aggregated by a Sequence object
getDeletionTolerance.Sequence
                        Get the deletion tolerance site-process
                        specific parameter for a collection of Site
                        objects aggregated by a Sequence object
getDist.ContinuousDeletor
                        Get the length sampling expression
getDist.ContinuousInsertor
                        Get the length sampling expression
getEdge.PhyloSim        Get and edge from the edge matrix
getEdges.PhyloSim       Get the edge matrix from a phylo object
                        aggregated by a PhyloSim object
getEquDist.GeneralSubstitution
                        Get the equilibrium distribution from a
                        GeneralSubstitution object
getEquDist.ToleranceSubstitution
                        Get the equilibrium distribution from a
                        ToleranceSubstitution object
getEventRate.GeneralSubstitution
                        Get the scaled rate of an event from a
                        GeneralSubstitution object
getEventRate.QMatrix    Get the unscaled rate of an event from a
                        QMatrix object
getEventRate.ToleranceSubstitution
                        Get the scaled rate of an event from a
                        ToleranceSubstitution object
getEventRateAtSite.GeneralSubstitution
                        Get the site spcific rate of an event from a
                        GeneralSubstitution object
getEventRateAtSite.ToleranceSubstitution
                        Get the site spcific rate of an event from a
                        ToleranceSubstitution object
getEvents.Sequence      Get the list of active Event objects for a set
                        of Site objects aggregated by a Sequence object
getEvents.Site          Get the list of active event objects given the
                        current state of the Site object
getEventsAtSite.FastFieldDeletor
                        Generate a deletion event object given the
                        state of the target site
getEventsAtSite.GY94    Generate the list of active Event objects for a
                        given attached Site object
getEventsAtSite.GeneralDeletor
                        Title
getEventsAtSite.GeneralInsertor
                        Generate insertion event object given the state
                        of the target site
getEventsAtSite.GeneralSubstitution
                        Generate the list of active Event objects for a
                        given attached Site object
getEventsAtSite.Process
                        Generate the list of active Event objects given
                        a Site object
getEventsAtSite.ToleranceSubstitution
                        Generate the list of active Event objects for a
                        given attached Site object
getGenerateBy.GeneralInsertor
                        Get the function object used for generating
                        inserts
getHandler.Event        Get the handler function of an Event object
getId.PhyloSim          Get the unique identifier of a PhyloSim object
getId.Process           Get the unique identifier of a Process object
getId.QMatrix           Get the unique identifier of a QMatrix object
getId.Sequence          Get the unique identifier of a Sequence object
getInsertHook.GeneralInsertor
                        Get the insert hook function
getInsertionTolerance.Sequence
                        Get the insertion tolerance site-process
                        specific parameter for a collection of Site
                        objects aggregated by a Sequence object
getKappa.F84            Get the transition transversion rate ratio
getKappa.GY94           Get the transition/transversion rate ratio
getLength.Sequence      Get the number of Site objects aggregated in a
                        Sequence object
getLengthParam1.FastFieldDeletor
                        Get the first length parameter
getLengthParam2.FastFieldDeletor
                        Get the second length parameter
getLogFile.PhyloSim     Get the name of the file used for logging
getLogLevel.PhyloSim    Get the log level from a PhyloSim object
getMatrix.QMatrix       Get the unscaled rate matrix form a QMatrix
                        object
getMaxLength.ContinuousDeletor
                        Get the maximum length
getMaxLength.ContinuousInsertor
                        Get the maximum length
getMethodsList.PSRoot   Get the list of applicable methods for an
                        object
getName.Event           Get the name of an Event object
getName.PhyloSim        Get the name of a PhyloSim object
getName.Process         Get the name of a Process object
getName.QMatrix         Get the name of a QMatrix object
getName.Sequence        Get the name of a Sequence object
getNedges.PhyloSim      Get the number of edges from phylo object
                        aggregated by a PhyloSim object
getNodes.PhyloSim       Get the node identifiers from a PhyloSim object
getNtips.PhyloSim       Get the number of the tips form a phylo object
                        aggregated by a PhyloSim object
getOmegaScalingFactor.GY94
                        Get the omega scaling factor
getOmegas.CodonSequence
                        Get the omegas from a collection of sites
getParameterAtSite.Process
                        Get the value of a site-process specific
                        paramter from a Site object attached to a
                        Process object
getParameterAtSites.Sequence
                        Get the values of a site-process specific
                        paramater for a process and a collection of
                        Site objects aggregated by a Sequence object
getPhylo.PhyloSim       Get the phylo object aggregated in a PhyloSim
                        object
getPosition.Event       Get the position of the Site object associated
                        to an Event object in the enclosing Sequence
                        object
getProbs.DiscreteDeletor
                        Get the deletion length probabilities
getProbs.DiscreteInsertor
                        Get the insertion length probabilities
getProcess.Event        Get the Process object which generated an Event
                        object
getProcess.QMatrix      Get the process object associated with a
                        QMatrix object
getProcesses.Sequence   Get the Process objects attached to the Site
                        objects aggregated by a Sequence object
getProcesses.Site       Get the list of Process objects attached to a
                        Site object
getProposeBy.GeneralInDel
                        Get the function used for proposing indel
                        lengths
getQMatrix.GeneralSubstitution
                        Get the QMatrix object aggregated by a
                        GeneralSubstitution object
getQMatrix.ToleranceSubstitution
                        Get the QMatrix object aggregated by a
                        ToleranceSubstitution object
getRate.Event           Get the rate of an Event object
getRate.GeneralInDel    Get the general rate
getRate.GeneralSubstitution
                        Get an unscaled rate of an event from a
                        GeneralSubstitution object
getRate.QMatrix         Get an unscaled rate of an event from a QMatrix
                        object
getRate.ToleranceSubstitution
                        Get an unscaled rate of an event from a
                        ToleranceSubstitution object
getRateList.GeneralSubstitution
                        Get a list of events and their unscaled rates
                        from a GeneralSubstitution object
getRateList.QMatrix     Get a list of events and their unscaled rates
                        from a QMatrix object
getRateList.ToleranceSubstitution
                        Get a list of events and their unscaled rates
                        from a ToleranceSubstitution object
getRateMultipliers.Sequence
                        Get the values of the rate multiplier
                        parameters for a given Process object and a
                        collection of Site object aggregated by a
                        Sequence object
getRateParam.F81        Forbidden action: the value of a rate
                        parameters
getRateParam.F84        Get the value of a rate parameter
getRateParam.GTR        Get the value of a rate parameter
getRateParam.HKY        Get the value of a rate parameter
getRateParam.K80        Get the value of a rate parameter
getRateParam.K81        Get the value of a rate parameter
getRateParam.T92        Get the value of a rate parameter
getRateParam.TN93       Get the value of a rate parameter
getRateParamList.F81    Forbidden action: getting the list of rate
                        parameters
getRateParamList.F84    Get the rate parameters
getRateParamList.GTR    Get the rate parameters
getRateParamList.HKY    Get the rate parameters
getRateParamList.K80    Get the rate parameters
getRateParamList.K81    Get the rate parameters
getRateParamList.T92    Get the rate parameters
getRateParamList.TN93   Get the rate parameters
getRootNode.PhyloSim    Get the identifier of the root node from a
                        PhyloSim object
getRootSeq.PhyloSim     Get the root sequence aggregated by a PhyloSim
                        object
getScale.BrownianInsertor
                        Get scale parameter
getScaledMatrix.QMatrix
                        Get the scaled rate matrix form a QMatrix
                        object
getSeqFromNode.PhyloSim
                        Get the Sequence object associated with a given
                        node of a phylo object aggregated by a PhyloSim
                        object
getSequence.Site        Get the Sequence object associated with a given
                        Site object
getSequences.PhyloSim   Gets all the Sequence objects associated with
                        the nodes of a phylo object aggregated by a
                        PhyloSim object
getSite.Event           Get the Site object associated with an Event
                        object
getSiteSpecificParamIds.Process
                        Get the site specific paramter identifiers from
                        a Process object
getSiteSpecificParamList.Process
                        Get the list of site specific parameters of a
                        Process object
getSites.Sequence       Get the list of the Site object aggregated in a
                        Sequence object
getSize.Alphabet        Get the number of symbols in an Alphabet object
getSizes.DiscreteDeletor
                        Get the sizes of the proposed deletions
getSizes.DiscreteInsertor
                        Get the sizes of the proposed insertions
getState.Site           Get the current state of a Site object
getStates.Sequence      Get the states of a set of Site objects
                        aggregated by a Sequence object
getString.Sequence      Get the string representation of a Sequence
                        object
getSymbolFreqs.Sequence
                        Get a table with the frequencies of the states
                        of a collection of Site objects aggregated by a
                        Sequence object
getSymbolLength.Alphabet
                        Get the length of the symbols in a given
                        alphabet object
getSymbols.Alphabet     Get the symbol set from an Alphabet object
getTableId.CodonAlphabet
                        Get the genetic code id
getTemplateSeq.GeneralInsertor
                        Get the template sequence object
getTheta.T92            Get the GC content
getTipLabels.PhyloSim   Get the tip labels from a phylo object
                        aggregated by a PhyloSim object
getTips.PhyloSim        Get the node identifiers of the tip nodes from
                        a PhyloSim object
getToleranceMargin.FastFieldDeletor
                        Get the tolerance margin
getTotalRate.Site       Get the total active event rate
getTotalRates.Sequence
                        Get the total site rates from a Sequence object
getTotalRatesFromRange.Sequence
                        Get the vector of total site rates for a
                        collection of Site objects aggregated by a
                        Sequence object
getTransTable.CodonAlphabet
                        Get the list storing the genetic code table
getTreeLength.PhyloSim
                        Get the tree length from a PhyloSim object
getType.Alphabet        Get Alphabet obejct type
getType.BrownianInsertor
                        Get the type of the BrownianInsertor process
getType.FastFieldDeletor
                        Get the type of a FastFieldDeletor object
getUniqueAlphabets.Sequence
                        Get the list of unique Alphabet objects
                        associated to Site objects aggaregated by a
                        Sequence object
getUniqueProcesses.Sequence
                        Get the list of unique Process instances
                        attached to the Site objects aggregated by a
                        Sequence object
getWriteProtected.Alphabet
                        Check if the object is write protected
getWriteProtected.Event
                        Check if the object is write protected
getWriteProtected.Process
                        Check if the object is write protected
getWriteProtected.QMatrix
                        Check if the object is write protected
getWriteProtected.Sequence
                        Check if the object is write protected
globalConsistencyCheck.PSRoot
                        Check the consistency of all objects inheriting
                        form PSRoot in the current environment
hasSiteSpecificParameter.Process
                        Check if a Process object has the site-process
                        specific parameter with the given id
hasSymbols.Alphabet     Check if an Alphabet object has a given set of
                        symbols
hasUndefinedRate.GeneralInDel
                        Check whether the general rate of a
                        GeneralInDel object is undefined
hasUndefinedRate.GeneralSubstitution
                        Check if a GeneralSubstitution object has
                        undefined rates
hasUndefinedRate.Process
                        Check if the Process object has undefined rate
                        parameters
hasUndefinedRate.ToleranceSubstitution
                        Check if a ToleranceSubstitution object has
                        undefined rates
insertSequence.Sequence
                        Insert a Sequence object into another Sequence
                        object after a specified position
intersect.list.PSRoot   Utility method returning the intersection of
                        two lists
is.Alphabet             Check if an object is an instance of the
                        Alphabet class
is.CodonAlphabet        Check if an object inherits from CodonAlphabet
is.CodonUNREST          Check whether an object inherits from
                        CodonUNREST
is.Event                Check whether an object inherits from the class
                        Event
is.GY94                 Check whether an object inherits from GY94
is.GeneralDeletor       Check whether an object inherits from
                        GeneralDeletor
is.GeneralInDel         Check if an object inherits from the
                        GeneralInDel class
is.GeneralInsertor      Check whether an object inherits from
                        GeneralInsertor
is.GeneralSubstitution
                        Check if an object is an instance of the
                        GeneralSubstitution class
is.PSRoot               Check if an object inherits from PSRoot
is.Process              Check if an object is an instance of the
                        Process class
is.QMatrix              Check if an object is an instance of the
                        QMatrix class
is.Sequence             Check whether an object inherits from the
                        Sequence class
is.Site                 Check if an object is an instance of the Site
                        class
is.ToleranceSubstitution
                        Check if an object is an instance of the
                        ToleranceSubstitution class
is.na.PSRoot            Check if a PSRoot object is NA
is.phylo                Check if an object is an instance of the phylo
                        class
is.tip.PhyloSim         Check if a node is a tip
isAttached.Site         Check whether a Process object is attached to a
                        Site object
isEmpty.Alphabet        Check if the symbol set is empty
isStartCodon.CodonAlphabet
                        Check if a codon is a start codon
isStopCodon.CodonAlphabet
                        Check if a codon is a stop codon
ll.PSRoot               Display detailed information about the virtual
                        fields and methods defined for a given object
mtArt                   The mtArt empirical amino acid substitution
                        model
mtMam                   The mtMam empirical amino acid substitution
                        model
mtREV24                 The mtREV24 empirical amino acid substitution
                        model
my.all.equal.PSRoot     Test if two objects are nearly equal
newAAMatrix.AminoAcidSubst
                        Undocumented method
newMatrix.CodonSubst    New codon substitution matrix from PAML file
omegaHist.CodonSequence
                        Plot a histogram of omega values from a range
omegaVarM0.CodonSequence
                        The M0 (one-ratio) model of variable omega
                        ratios among sites
omegaVarM1.CodonSequence
                        The M1 (neutral) model of variable omega ratios
                        among sites
omegaVarM2.CodonSequence
                        The M2 (selection) model of variable omega
                        ratios among sites
omegaVarM3.CodonSequence
                        The M3 (discrete) model of variable omega
                        ratios among sites
omegaVarM4.CodonSequence
                        The M4 (freqs) model of variable omega ratios
                        among sites
plot.ContinuousDeletor
                        Plot the density of proposed lengths
plot.ContinuousInsertor
                        Plot the density of proposed lengths
plot.DiscreteDeletor    Plot the deletion length distribution
plot.DiscreteInsertor   Plot the insertion length distribution
plot.GeneralSubstitution
                        Create a bubble plot of the substitution
                        process
plot.PhyloSim           Plot a PhyloSim object
plot.Sequence           Plot the total site rates for a collection of
                        Site objects aggregated by a Sequence object
plot.ToleranceSubstitution
                        Create a bubble plot of the substitution
                        process
plotParametersAtSites.Sequence
                        Plot the value of a site-process specifc
                        paramter for a collection of Site objects
                        aggregated by a Sequence object
plusGamma.Sequence      Sample the rate multiplier parameters of a
                        Process from a Gamma distribution for a
                        collection of Site objects aggregated by a
                        Sequence object
plusInvGamma.Sequence   Sample the rate multiplier parameters of a
                        Process from an I+Gamma distribution for a
                        collection of Site objects aggregated by a
                        Sequence object
print.PSRootSummary     Print out a PSRootSummary object
print.QMatrix           Print the character representation of a QMatrix
                        object
proposeLength.GeneralInDel
                        Propose indel length
readAlignment.PhyloSim
                        Read alignment from file
readTree.PhyloSim       Read tree from file
rescaleQMatrix.GeneralSubstitution
                        Rescale the scaled rate matrix of a QMatrix
                        object aggregated by a GeneralSubstitution
                        object
rescaleQMatrix.ToleranceSubstitution
                        Rescale the scaled rate matrix of a QMatrix
                        object aggregated by a ToleranceSubstitution
                        object
revComp.NucleotideSequence
                        Reverse complmenet a NucleotideSequence object
sampleState.GeneralSubstitution
                        Sample a state from the equlibrium distribution
                        of a GeneralSubstitution object
sampleState.ToleranceSubstitution
                        Sample a state from the equlibrium distribution
                        of a ToleranceSubstitution object
sampleStates.Sequence   Sample the states for a collection of Site
                        objects aggregated by a Sequence object
saveAlignment.PhyloSim
                        Save the alignment stored in a PhyloSim object
                        in a Fasta file
scaleTree.PhyloSim      Scale the branch lengths of a phylo object
                        aggragted by a PhyloSim object
setAcceptBy.GeneralInDel
                        Set the function used for accepting/rejecting
                        indel events
setAcceptWin.GeneralInsertor
                        Set the size of the acceptance window
setAlignment.PhyloSim   Forbidden action: setting the alignment stored
                        in a PhyloSim object
setAlphabet.GeneralSubstitution
                        Set the Alphabet object aggregated by a
                        GeneralSubstitution object
setAlphabet.Process     Assotiate an Alphabet object with a Process
                        object
setAlphabet.QMatrix     Set the Alphabet object for a QMatrix object
setAlphabet.Site        Attach an Alphabet object to a Site object
setAlphabet.ToleranceSubstitution
                        Set the Alphabet object aggregated by a
                        ToleranceSubstitution object
setAlphabets.Sequence   Assotiate Alphabet objects to a set of Site
                        objects aggregated by a Sequence object
setAncestral.Sequence   Set the ancestral object of a Sequence object
setAncestral.Site       Forbidden action: setting the ancestral object
                        for a Site object
setBaseFreqs.F81        Set the base frequency parameters
setBaseFreqs.F84        Set the base frequency parameters
setBaseFreqs.GTR        Set the base frequency parameters
setBaseFreqs.HKY        Set the base frequency parameters
setBaseFreqs.K80        Forbidden action: setting the base frequency
                        parameters for a K80 object
setBaseFreqs.K81        Forbidden action: setting the base frequency
                        parameters for a K81 model
setBaseFreqs.TN93       Set the base frequency parameters
setBigRate.Sequence     Forbidden action: setting the sum of total
                        active event rates for a Sequence object
setBranchEvents.PhyloSim
                        Forbidden action: setting the list of events
                        having per-branch statistics recorded
setCodonFreqs.GY94      Get codon frequencies
setComments.PSRoot      Set the comments associated with an object
setCumulativeRates.Sequence
                        Forbidden action: setting the cumulative rates
                        for the sites aggregated by a Sequence object
setDeletionTolerance.Sequence
                        Set the deletion tolerance site-process
                        specific parameter for a collection of Site
                        objects aggregated by a Sequence object
setDist.ContinuousDeletor
                        Set the length sampling expression
setDist.ContinuousInsertor
                        Set the length sampling expression
setEdges.PhyloSim       Forbidden action: setting the edge matrix for a
                        phylo object aggregated by a PhyloSim object
setEquDist.GeneralSubstitution
                        Set the equilibrium distribution for a
                        GeneralSubstitution object
setEquDist.ToleranceSubstitution
                        Set the equilibrium distribution for a
                        ToleranceSubstitution object
setEvents.Site          Forbidden action: setting the list of active
                        events for a Site object
setGenerateBy.GeneralInsertor
                        Set the function object used for generating
                        inserts
setHandler.Event        Forbidden action: setting the handler function
                        of an Event object
setId.PhyloSim          Forbidden action: setting the unique identifier
                        of a PhyloSim object
setId.Process           Forbidden action: setting the unique Process
                        object identifier
setId.QMatrix           Forbidden action: setting the unique identifier
                        for a QMatrix object
setId.Sequence          Forbidden action: setting the unique identifier
                        of a Sequence object
setInsertHook.GeneralInsertor
                        Set the insert hook function
setInsertionTolerance.Sequence
                        Set the insertion tolerance site-process
                        specific parameter for a collection of Site
                        objects aggregated by a Sequence object
setKappa.F84            Get the transition transversion rate ratio
setKappa.GY94           Set the transition/transversion rate ratio
setLength.Sequence      Forbidden action: setting the length of a
                        Sequence object
setLengthParam1.FastFieldDeletor
                        Set the first length parameter
setLengthParam2.FastFieldDeletor
                        Set the second length parameter
setLogFile.PhyloSim     Set the name of the file used for logging
setLogLevel.PhyloSim    Set the log level for a given PhyloSim object
setMatrix.QMatrix       Forbidden action: setting the unscaled rate
                        matrix for a QMatrix object
setMaxLength.ContinuousDeletor
                        Set the maximum length
setMaxLength.ContinuousInsertor
                        Set the maximum length
setMethodsList.PSRoot   Forbidden action: setting the list of
                        applicable methods for an object
setName.Event           Set the name of an Event object
setName.PhyloSim        Set the name of a PhyloSim object
setName.Process         Set the name of a Process object
setName.QMatrix         Set the name of a QMatrix object
setName.Sequence        Set the name of a Sequence object
setNedges.PhyloSim      Forbidden action: setting the number of edges
                        for phylo object aggregated by a PhyloSim
                        object
setNodes.PhyloSim       Forbidden action: setting the node identifiers
                        for a PhyloSim object
setNtips.PhyloSim       Forbidden action: setting the number of the
                        tips for a phylo object aggregated by a
                        PhyloSim object
setOmegas.CodonSequence
                        Set the omegas for a collection of sites
setParameterAtSite.Process
                        Set the value of a site-process specific
                        paramter in a Site object attached to a Process
                        object
setParameterAtSites.Sequence
                        Set the values of a site-process specific
                        paramater for a process and a collection of
                        Site objects aggregated by a Sequence object
setPhylo.PhyloSim       Set the phylo object for a PhyloSim object
setPosition.Event       Set the position of the Site object associated
                        to an Event object
setProbs.DiscreteDeletor
                        Set the deletion length probabilities
setProbs.DiscreteInsertor
                        Set the insertion length probabilities
setProcess.Event        Set the generator process for an Event object
setProcess.QMatrix      Assotiate a process object with a QMatrix
                        object
setProcesses.Sequence   Specify a set of Process objects to be attached
                        to a set of Site objects aggregated by a
                        Sequence object
setProcesses.Site       Specify the list of Process objects attached to
                        a Site object
setProposeBy.GeneralInDel
                        Set the function used for proposing indel
                        lengths
setQMatrix.GeneralSubstitution
                        Set the QMatrix object aggregated by a
                        GeneralSubstitution object
setQMatrix.ToleranceSubstitution
                        Set the QMatrix object aggregated by a
                        ToleranceSubstitution object
setRate.Event           Set the rate of an Event object
setRate.GY94            Set an unscaled rate for an event from a GY94
                        object
setRate.GeneralInDel    Set the general rate
setRate.GeneralSubstitution
                        Set an unscaled rate for an event from a
                        GeneralSubstitution object
setRate.QMatrix         Set an unscaled rate in a QMatrix object
setRate.ToleranceSubstitution
                        Set an unscaled rate for an event from a
                        ToleranceSubstitution object
setRateList.GeneralSubstitution
                        Setting the rates for a GeneralSubstitution
                        object
setRateList.QMatrix     Setting the unscaled rates stored in a QMatrix
                        object
setRateList.ToleranceSubstitution
                        Setting the rates for a ToleranceSubstitution
                        object
setRateMultipliers.Sequence
                        Set the values of the rate multiplier
                        parameters for a given Process object and a
                        collection of Site object aggregated by a
                        Sequence object
setRateParam.F81        Forbidden action: getting the list of rate
                        parameters
setRateParam.F84        Set the value of a rate parameter
setRateParam.GTR        Set the value of a rate parameter
setRateParam.HKY        Set the value of a rate parameter
setRateParam.K80        Set the value of a rate parameter
setRateParam.K81        Set the value of a rate parameter
setRateParam.T92        Set the value of a rate parameter
setRateParam.TN93       Set the value of a rate parameter
setRateParamList.F81    Forbidden action: getting the list of rate
                        parameters
setRateParamList.F84    Set the rate parameters
setRateParamList.GTR    Set the rate parameters
setRateParamList.HKY    Set the rate parameters
setRateParamList.K80    Set the rate parameters
setRateParamList.K81    Set the rate parameters
setRateParamList.T92    Set the rate parameters
setRateParamList.TN93   Set the rate parameters
setRootNode.PhyloSim    Forbidden action: setting the identifier of the
                        root node for a PhyloSim object
setRootSeq.PhyloSim     Set the root sequence for a PhyloSim object
setScale.BrownianInsertor
                        Set scale parameter
setScaledMatrix.QMatrix
                        Forbidden action: setting the scaled rate
                        matrix for a QMatrix object
setSequence.Site        Assotiate a Sequence object with a Site object
setSequences.PhyloSim   Forbidden action: setting the Sequence objects
                        associated with the nodes of a phylo object
                        aggregated by a PhyloSim object
setSite.Event           Assotiate an Event object with a Site object
setSiteSpecificParamIds.Process
                        Forbidden action: setting the paramter
                        identifiers of the site specific paramters from
                        a Process object
setSiteSpecificParamList.Process
                        Forbidden action: setting the site specific
                        paramter list for a Process object
setSize.Alphabet        Forbidden action: setting the symbol set size
                        of an Alphabet object
setSizes.DiscreteDeletor
                        Set the sizes of the proposed deletions
setSizes.DiscreteInsertor
                        Set the sizes of the proposed insertions
setState.Site           Set the state of a Site object
setStates.Sequence      Set the states for a set of Site objects
                        aggregated by a Sequence object
setString.Sequence      Forbidden action: setting the string
                        representation of a Sequence object
setSymbolLength.Alphabet
                        Forbidden action: setting the symbol length for
                        an Alphabet object
setSymbols.Alphabet     Specify a new symbol set for an Alphabet object
setTableId.CodonAlphabet
                        Forbidden action: setting the genetic code id
setTemplateSeq.GeneralInsertor
                        Set the template sequence object
setTheta.T92            Set the GC content
setTipLabels.PhyloSim   Forbidden action: setting the tip labels for a
                        phylo object aggregated by a PhyloSim object
setTips.PhyloSim        Forbidden action: setting the node identifiers
                        of the tip nodes for a PhyloSim object
setToleranceMargin.FastFieldDeletor
                        Set the tolerance margin
setTotalRate.Site       Forbidden action: setting the total active
                        event rate for a Site object
setTotalRates.Sequence
                        Forbidden action: setting the list of total
                        site rates for a Sequence object
setTransTable.CodonAlphabet
                        Forbidden action: setting the genetic code
                        table for a CodonAlphabet object
setTreeLength.PhyloSim
                        Forbidden action: setting the tree length for a
                        PhyloSim object
setType.Alphabet        Set Alphabet object type
setType.BrownianInsertor
                        Forbidden action: setting the type of a
                        BrownianInsertor object
setType.FastFieldDeletor
                        Forbidden action: setting the type of a
                        FastFieldDeletor object
setUniqueAlphabets.Sequence
                        Forbidden action: setting the list of unique
                        Alphabet objects attached to the Site object
                        aggregated by a Sequence object
setUniqueProcesses.Sequence
                        Forbidden action: setting the list of unique
                        Process instances attached to the sites of a
                        Sequence object
setWriteProtected.Alphabet
                        Set the write protection field for an object
setWriteProtected.Event
                        Set the write protection field for an object
setWriteProtected.Process
                        Set the write protection field for an object
setWriteProtected.QMatrix
                        Set the write protection field for a QMatrix
                        object
setWriteProtected.Sequence
                        Set the write protection field for an object
stringLength            Returns the string length of the character
                        representation of an object
stringLengthVector      Returns the string lengths of the character
                        represenations of a collection of objects
summary.Alphabet        Summarize the properties of an object
summary.AminoAcidSubst
                        Summarize the properties of an object
summary.BinarySubst     Summarize the properties of an object
summary.BrownianInsertor
                        Summarize the properties of an object
summary.CodonAlphabet   Summarize the properties of an object
summary.CodonSubst      Summarize the properties of an object
summary.ContinuousDeletor
                        Summarize the properties of an object
summary.ContinuousInsertor
                        Summarize the properties of an object
summary.DiscreteDeletor
                        Summarize the properties of an object
summary.DiscreteInsertor
                        Summarize the properties of an object
summary.Event           Summarize the properties of an object
summary.F81             Summarize the properties of an object
summary.F84             Summarize the properties of an object
summary.FastFieldDeletor
                        Summarize the properties of an object
summary.GTR             Summarize the properties of an object
summary.GY94            Summarize the properties of an object
summary.GeneralDeletor
                        Summarize the properties of an object
summary.GeneralInDel    Summarize the properties of an object
summary.GeneralInsertor
                        Summarize the properties of an object
summary.GeneralSubstitution
                        Summarize the properties of an object
summary.HKY             Summarize the properties of an object
summary.JC69            Summarize the properties of an object
summary.K80             Summarize the properties of an object
summary.K81             Summarize the properties of an object
summary.PSRoot          Summarize the properties of an object
summary.PhyloSim        Summarize the properties of an object
summary.Process         Summarize the properties of an object
summary.QMatrix         Summarize the properties of an object
summary.Sequence        Summarize the properties of an object
summary.Site            Summarize the properties of an object
summary.T92             Summarize the properties of an object
summary.TN93            Summarize the properties of an object
summary.ToleranceSubstitution
                        Summarize the properties of an object
summary.UNREST          Summarize the properties of an object
translateCodon.CodonAlphabet
                        Translate a codon
virtualAssignmentForbidden.PSRoot
                        Throws an error message informing the user
                        about forbidden action on virtual a field
