The BinarySubst class
Check whether the two supplied Process objects are identical
The BinaryAlphabet class
The AnyAlphabet class
The Alphabet class
The AminoAcidSequence class
Check if two alaphabet objects have the same symbol set
The BinarySequence class
The AminoAcidAlphabet class
The AminoAcidSubst class
Save a debug message in the PhyloSim log file
The CodonSubst class
The ContinuousDeletor class
The BrownianInsertor class
The ECMunrest empirical codon substitution model
The ContinuousInsertor class
The Event class
BrownianPath.BrownianInsertor
Generate a Brownian path
The F81 class
The F84 class
The CodonAlphabet class
The CodonSequence class
The DiscreteInsertor class
The ECMrest empirical codon substitution model
The K81 class
The LG empirical amino acid substitution model
The GeneralInDel class
The CodonUNREST class
The FastFieldDeletor class
The DiscreteDeletor class
The GTR class
The QMatrix class
The PSRootSummary class
The root class for all phylosim objects
The Process class
The JTT.dcmut empirical amino acid substitution model
The K80 class
The MtZoa empirical amino acid substitution model
Save a message in the PhyloSim log file
The GeneralDeletor class
The GY94 class
The JC69 class
The JTT empirical amino acid substitution model
The NucleotideAlphabet class
The GeneralSubstitution class
The GeneralInsertor class
The PAM empirical amino acid substitution model
The PAM.dcmut empirical amino acid substitution model
The WAG empirical amino acid substitution model
Perform an event
The HKY class
The PhyloSim class
The NucleotideSequence class
The ToleranceSubstitution class
The Sequence class
Scale the scaled rate matrix stored in a QMatrix object by the provided factor
Run a simulation according to a PhyloSim object
areSynonymous.CodonAlphabet
Check whether two codons are synonymous
The T92 class
The TN93 class
The UNREST class
checkConsistency.Alphabet
Check object consistency
checkConsistency.DiscreteDeletor
Check object consistency
Get the character representation of an Event object
Get the character representation of an Alphabet object
checkConsistency.ContinuousInsertor
Check object consistency
Build rate matrix from PAML file
Translate a CodonSequence object
Return the character representation of a PhyloSim object
as.character.GeneralSubstitution
Return the character representation of a GeneralSubstitution object
Assotiate a Sequence object with a given node of a phylo object aggregated by a PhyloSim object
The Site class
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
checkConsistency.CodonSequence
Check object consistency
Check object consistency
buildFromPAML.AminoAcidSubst
Build rate matrix from PAML file
checkConsistency.DiscreteInsertor
Check object consistency
Check object consistency
checkConsistency.AminoAcidSubst
Check object consistency
Attach a Process object to a set of Site objects aggregated by a Sequence object
Return the character representation of a QMatrix object
Get the character representation of a Process object
Get the string representation of a Sequence object
Get the character representation of a Site object
checkConsistency.BrownianInsertor
Check object consistency
Undocumented object (PhyloSim package)
checkConsistency.CodonSubst
Check object consistency
checkConsistency.CodonAlphabet
Check object consistency
Check object consistency
Attach a Process object to a Site object
checkConsistency.CodonUNREST
Check object consistency
Check object consistency
checkConsistency.FastFieldDeletor
Check object consistency
checkConsistency.ContinuousDeletor
Check object consistency
Clone a process object
checkConsistency.GeneralInsertor
Check object consistency
checkConsistency.GeneralInDel
Check object consistency
Check object consistency
checkConsistency.BinarySubst
Check object consistency
Check object consistency
Clone a Sequence object
checkConsistency.GeneralSubstitution
Check object consistency
Check object consistency
Check object consistency
Check object consistency
The cpREV empirical amino acid substitution model
checkConsistency.GeneralDeletor
Check object consistency
Check object consistency
clone.ToleranceSubstitution
Clone a ToleranceSubstitution object
Check object consistency
Check object consistency
Copy a collection of Site objects aggregated by a Sequence object into a new Sequence object
deleteSubSequence.Sequence
Delete a collection of sites aggregated by a Sequence object
Get the Alphabet object associated with a QMatrix object
generateInsert.GeneralInsertor
Generate an insert
Flag the total event rate
checkConsistency.PSRootSummary
Check object consistency
Set the states of a collection of Site objects aggregated by a Sequence object to undefined (NA)
checkConsistency.PhyloSim
Check object consistency
clone.GeneralSubstitution
Clone a GeneralSubstitution object
Export the per-branch counts of an event as a phylo object
Get the Alphabet object attached to a Site object
Enable the use of virtual fields for a given object
checkConsistency.ToleranceSubstitution
Check object consistency
Check object consistency
Site
Get the alignment stored in a PhyloSim object
Check object consistency
detachSeqFromNode.PhyloSim
Detach a Sequence object from a given node of a phylo object aggregated by a PhyloSim object
getAlignmentLength.PhyloSim
Get the alignment length from a PhyloSim object
Get the function used for accepting/rejecting indel events
getAcceptWin.GeneralInsertor
Get the size of the acceptance window
Get the base frequency parameters
Get the base frequency parameters
getCumulativeRatesFromRange.Sequence
Get the cumulative site rates for a collection of Site objects aggregated by a Sequence object
Get the base frequency parameters
getDeletionTolerance.Sequence
Get the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
Get the base frequency parameters
Check object consistency
Get the base frequency parameters
getAlphabet.ToleranceSubstitution
Get the Alphabet object aggregated by a ToleranceSubstitution object
Get codon frequencies
Get the list of events having per-branch statistics recorded
Get the list of the Alphabet objects attached to the Site objects aggregated by a Sequence object
getCumulativeRates.Sequence
Get the total site rates from a Sequence object
Get the comments associated with an object
Get the base frequency parameters
checkConsistency.Sequence
Check object consistency
Check object consistency
Get the list of active Event objects for a set of Site objects aggregated by a Sequence object
getEventRateAtSite.ToleranceSubstitution
Get the site spcific rate of an event from a ToleranceSubstitution object
Get the edge matrix from a phylo object aggregated by a PhyloSim object
Get and edge from the edge matrix
detachHookFromNode.PhyloSim
Detach a node hook function from a given node of a phylo object aggregated by a PhyloSim object
getAlphabet.GeneralSubstitution
Get the Alphabet object aggregated by a GeneralSubstitution object
Detach a Process object from a set of Site objects aggregated by a Sequence object
Get the ancestral object of a Sequence object
Get the sum of all active event rates from a Sequence object
Get the base frequency parameters
Get the ancestral object of a Site object
Get the Alphabet object associated with a given Process object
getEventRateAtSite.GeneralSubstitution
Get the site spcific rate of an event from a GeneralSubstitution object
getDist.ContinuousInsertor
Get the length sampling expression
getEventRate.ToleranceSubstitution
Get the scaled rate of an event from a ToleranceSubstitution object
getDist.ContinuousDeletor
Get the length sampling expression
getEventRate.GeneralSubstitution
Get the scaled rate of an event from a GeneralSubstitution object
Get the unscaled rate of an event from a QMatrix object
Generate the list of active Event objects for a given attached Site object
getEventsAtSite.GeneralDeletor
Title
getEventsAtSite.GeneralSubstitution
Generate the list of active Event objects for a given attached Site object
getEventsAtSite.GeneralInsertor
Generate insertion event object given the state of the target site
getInsertHook.GeneralInsertor
Get the insert hook function
Get the unique identifier of a QMatrix object
getLengthParam2.FastFieldDeletor
Get the second length parameter
Get the unique identifier of a Sequence object
getInsertionTolerance.Sequence
Get the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
Get the list of active event objects given the current state of the Site object
Get the list of applicable methods for an object
getEventsAtSite.FastFieldDeletor
Generate a deletion event object given the state of the target site
Get the name of the file used for logging
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
getLengthParam1.FastFieldDeletor
Get the first length parameter
getEquDist.GeneralSubstitution
Get the equilibrium distribution from a GeneralSubstitution object
Get the number of Site objects aggregated in a Sequence object
getEquDist.ToleranceSubstitution
Get the equilibrium distribution from a ToleranceSubstitution object
getGenerateBy.GeneralInsertor
Get the function object used for generating inserts
Get the handler function of an Event object
Get the Process objects attached to the Site objects aggregated by a Sequence object
Get the name of a PhyloSim object
Get the name of a Process object
Get the number of edges from phylo object aggregated by a PhyloSim object
Get the node identifiers from a PhyloSim object
Get the number of the tips form a phylo object aggregated by a PhyloSim object
Get the name of an Event object
getOmegaScalingFactor.GY94
Get the omega scaling factor
Get the transition transversion rate ratio
Get the transition/transversion rate ratio
getEventsAtSite.ToleranceSubstitution
Generate the list of active Event objects for a given attached Site object
Get the unique identifier of a Process object
Get the unique identifier of a PhyloSim object
Generate the list of active Event objects given a Site object
Get the process object associated with a QMatrix object
getMaxLength.ContinuousDeletor
Get the maximum length
Get the phylo object aggregated in a PhyloSim object
getMaxLength.ContinuousInsertor
Get the maximum length
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
Get the value of a rate parameter
Get the list of Process objects attached to a Site object
Get the log level from a PhyloSim object
Get the position of the Site object associated to an Event object in the enclosing Sequence object
Get the Sequence object associated with a given node of a phylo object aggregated by a PhyloSim object
Get the name of a QMatrix object
Get the unscaled rate matrix form a QMatrix object
Get the name of a Sequence object
Get the rate of an Event object
Get the value of a rate parameter
Get the sizes of the proposed deletions
Get the deletion length probabilities
Get the general rate
Get the tip labels from a phylo object aggregated by a PhyloSim object
getProposeBy.GeneralInDel
Get the function used for proposing indel lengths
Get the Process object which generated an Event object
getProbs.DiscreteInsertor
Get the insertion length probabilities
Get the root sequence aggregated by a PhyloSim object
getScale.BrownianInsertor
Get scale parameter
getQMatrix.GeneralSubstitution
Get the QMatrix object aggregated by a GeneralSubstitution object
Get an unscaled rate of an event from a QMatrix object
Forbidden action: getting the list of rate parameters
getRate.GeneralSubstitution
Get an unscaled rate of an event from a GeneralSubstitution object
getQMatrix.ToleranceSubstitution
Get the QMatrix object aggregated by a ToleranceSubstitution object
Get the states of a set of Site objects aggregated by a Sequence 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
Get the value of a rate parameter
Get Alphabet obejct type
Get the number of symbols in an Alphabet object
globalConsistencyCheck.PSRoot
Check the consistency of all objects inheriting form PSRoot in the current environment
Get the type of the BrownianInsertor process
Get the rate parameters
getTemplateSeq.GeneralInsertor
Get the template sequence object
Get the scaled rate matrix form a QMatrix object
Get the GC content
Get a list of events and their unscaled rates from a QMatrix object
Get the length of the symbols in a given alphabet object
Get the rate parameters
getSiteSpecificParamList.Process
Get the list of site specific parameters of a Process object
Get the list of the Site object aggregated in a Sequence object
hasSiteSpecificParameter.Process
Check if a Process object has the site-process specific parameter with the given id
Check if a node is a tip
Get the node identifiers of the tip nodes from a PhyloSim 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
Get the identifier of the root node from a PhyloSim object
Get the rate parameters
Get the total site rates from a Sequence object
Forbidden action: the value of a rate parameters
Get the Site object associated with an Event object
getRateList.ToleranceSubstitution
Get a list of events and their unscaled rates from a ToleranceSubstitution object
Check if an object inherits from the GeneralInDel class
getSiteSpecificParamIds.Process
Get the site specific paramter identifiers from a Process object
hasUndefinedRate.ToleranceSubstitution
Check if a ToleranceSubstitution object has undefined rates
Get the string representation of a Sequence object
Get the rate parameters
Get the value of a rate parameter
Get the value of a rate parameter
Utility method returning the intersection of two lists
Check if an Alphabet object has a given set of symbols
Get the type of a FastFieldDeletor object
Get the value of a rate parameter
Get the value of a rate parameter
Get the Sequence object associated with a given Site object
getWriteProtected.Sequence
Check if the object is write protected
Get the rate parameters
getTransTable.CodonAlphabet
Get the list storing the genetic code table
Check whether an object inherits from GeneralDeletor
Check whether an object inherits from CodonUNREST
Check if an object inherits from CodonAlphabet
Get a table with the frequencies of the states of a collection of Site objects aggregated by a Sequence object
Get the current state of a Site object
getSizes.DiscreteInsertor
Get the sizes of the proposed insertions
Get the genetic code id
getToleranceMargin.FastFieldDeletor
Get the tolerance margin
Plot the density of proposed lengths
Get the symbol set from an Alphabet object
Check whether a Process object is attached to a Site object
The M0 (one-ratio) model of variable omega ratios among sites
Get the rate parameters
Plot a histogram of omega values from a range
Get the rate parameters
Get the total active event rate
Check whether an object inherits from GeneralInsertor
Check whether an object inherits from the class Event
getWriteProtected.QMatrix
Check if the object is write protected
hasUndefinedRate.GeneralInDel
Check whether the general rate of a GeneralInDel object is undefined
getTotalRatesFromRange.Sequence
Get the vector of total site rates for a collection of Site objects aggregated by a Sequence object
Gets all the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim 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
Get the tree length from a PhyloSim object
Check if the object is write protected
getWriteProtected.Process
Check if the object is write protected
Insert a Sequence object into another Sequence object after a specified position
Check if an object is an instance of the QMatrix class
Check whether an object inherits from the Sequence class
Check if an object is an instance of the Site class
Check if an object is an instance of the GeneralSubstitution class
Check whether an object inherits from GY94
The mtREV24 empirical amino acid substitution model
Check if an object is an instance of the ToleranceSubstitution class
Read alignment from file
The mtArt empirical amino acid substitution model
Sample the states for a collection of Site objects aggregated by a Sequence object
Check if the Process object has undefined rate parameters
The mtMam empirical amino acid substitution model
Check if an object is an instance of the Alphabet class
setAcceptWin.GeneralInsertor
Set the size of the acceptance window
Check if an object is an instance of the phylo class
plotParametersAtSites.Sequence
Plot the value of a site-process specifc paramter for a collection of Site objects aggregated by a Sequence object
Sample the rate multiplier parameters of a Process from an I+Gamma distribution for a collection of Site objects aggregated by a Sequence object
getWriteProtected.Alphabet
Check if the object is write protected
isStopCodon.CodonAlphabet
Check if a codon is a stop codon
Sample the rate multiplier parameters of a Process from a Gamma distribution for a collection of Site objects aggregated by a Sequence object
Read tree from file
Test if two objects are nearly equal
Plot the density of proposed lengths
Check if an object is an instance of the Process class
hasUndefinedRate.GeneralSubstitution
Check if a GeneralSubstitution object has undefined rates
Print out a PSRootSummary object
Display detailed information about the virtual fields and methods defined for a given object
Check if an object inherits from PSRoot
setLengthParam2.FastFieldDeletor
Set the second length parameter
The M3 (discrete) model of variable omega ratios among sites
Set the function used for accepting/rejecting indel events
Check if a PSRoot object is NA
Plot a PhyloSim object
setEquDist.GeneralSubstitution
Set the equilibrium distribution for a GeneralSubstitution object
Set the base frequency parameters
sampleState.ToleranceSubstitution
Sample a state from the equlibrium distribution of a ToleranceSubstitution object
Forbidden action: setting the base frequency parameters for a K80 object
Forbidden action: setting the ancestral object for a Site object
Plot the deletion length distribution
The M4 (freqs) model of variable omega ratios among sites
Plot the insertion length distribution
newAAMatrix.AminoAcidSubst
Undocumented method
Check if the symbol set is empty
setDist.ContinuousDeletor
Set the length sampling expression
setDist.ContinuousInsertor
Set the length sampling expression
isStartCodon.CodonAlphabet
Check if a codon is a start codon
Forbidden action: setting the edge matrix for a phylo object aggregated by a PhyloSim object
Set the name of a Process object
setCumulativeRates.Sequence
Forbidden action: setting the cumulative rates for the sites aggregated by a Sequence object
Create a bubble plot of the substitution process
Set the base frequency parameters
New codon substitution matrix from PAML file
setDeletionTolerance.Sequence
Set the deletion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
revComp.NucleotideSequence
Reverse complmenet a NucleotideSequence object
The M1 (neutral) model of variable omega ratios among sites
The M2 (selection) model of variable omega ratios among sites
rescaleQMatrix.ToleranceSubstitution
Rescale the scaled rate matrix of a QMatrix object aggregated by a ToleranceSubstitution 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
Get the transition transversion rate ratio
Set the name of a PhyloSim object
Set the transition/transversion rate ratio
setParameterAtSite.Process
Set the value of a site-process specific paramter in a Site object attached to a Process object
Plot the total site rates for a collection of Site objects aggregated by a Sequence object
Set the name of the file used for logging
Print the character representation of a QMatrix object
Forbidden action: setting the unique identifier for a QMatrix object
Forbidden action: setting the unique identifier of a Sequence object
rescaleQMatrix.GeneralSubstitution
Rescale the scaled rate matrix of a QMatrix object aggregated by a GeneralSubstitution object
Set the rate of an Event object
plot.ToleranceSubstitution
Create a bubble plot of the substitution process
setMaxLength.ContinuousDeletor
Set the maximum length
setMaxLength.ContinuousInsertor
Set the maximum length
Assotiate an Alphabet object with a Process object
proposeLength.GeneralInDel
Propose indel length
Set the base frequency parameters
sampleState.GeneralSubstitution
Sample a state from the equlibrium distribution of a GeneralSubstitution object
setAlphabet.ToleranceSubstitution
Set the Alphabet object aggregated by a ToleranceSubstitution object
Save the alignment stored in a PhyloSim object in a Fasta file
setQMatrix.ToleranceSubstitution
Set the QMatrix object aggregated by a ToleranceSubstitution object
Set the omegas for a collection of sites
Forbidden action: setting the number of the tips for a phylo object aggregated by a PhyloSim object
Set the Alphabet object for a QMatrix object
Set the states for a set of Site objects aggregated by a Sequence object
setInsertHook.GeneralInsertor
Set the insert hook function
Forbidden action: setting the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object
Set the phylo object for a PhyloSim 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
Forbidden action: getting the list of rate parameters
Forbidden action: setting the genetic code id
Set the root sequence for a PhyloSim object
Attach an Alphabet object to a Site object
Scale the branch lengths of a phylo object aggragted by a PhyloSim object
setTransTable.CodonAlphabet
Forbidden action: setting the genetic code table for a CodonAlphabet object
Get codon frequencies
Forbidden action: setting the alignment stored in a PhyloSim object
setAlphabet.GeneralSubstitution
Set the Alphabet object aggregated by a GeneralSubstitution object
Specify a new symbol set for an Alphabet object
Set the base frequency parameters
Forbidden action: setting the base frequency parameters for a K81 model
Forbidden action: setting the number of edges for phylo object aggregated by a PhyloSim object
Forbidden action: setting the sum of total active event rates for a Sequence object
setEquDist.ToleranceSubstitution
Set the equilibrium distribution for a ToleranceSubstitution object
Set the base frequency parameters
Forbidden action: setting the list of active events for a Site object
setQMatrix.GeneralSubstitution
Set the QMatrix object aggregated by a GeneralSubstitution object
setProposeBy.GeneralInDel
Set the function used for proposing indel lengths
Set the log level for a given PhyloSim object
Forbidden action: setting the list of events having per-branch statistics recorded
Assotiate Alphabet objects to a set of Site objects aggregated by a Sequence object
Set the comments associated with an object
Set the value of a rate parameter
Forbidden action: setting the handler function of an Event object
setGenerateBy.GeneralInsertor
Set the function object used for generating inserts
Forbidden action: setting the unique identifier of a PhyloSim object
Set the ancestral object of a Sequence object
Set the value of a rate parameter
Set the value of a rate parameter
setLengthParam1.FastFieldDeletor
Set the first length parameter
Forbidden action: setting the unique Process object identifier
Set the generator process for an Event object
setRateList.ToleranceSubstitution
Setting the rates for a ToleranceSubstitution object
Assotiate an Event object with a Site object
Set the position of the Site object associated to an Event object
Forbidden action: setting the list of applicable methods for an object
setInsertionTolerance.Sequence
Set the insertion tolerance site-process specific parameter for a collection of Site objects aggregated by a Sequence object
Set the name of an Event object
Set the value of a rate parameter
Summarize the properties of an object
Setting the unscaled rates stored in a QMatrix object
setTemplateSeq.GeneralInsertor
Set the template sequence object
Summarize the properties of an object
Summarize the properties of an object
Set the GC content
Forbidden action: setting the tip labels for a phylo object aggregated by a PhyloSim object
setWriteProtected.QMatrix
Set the write protection field for a QMatrix object
Set the rate parameters
Summarize the properties of an object
setWriteProtected.Sequence
Set the write protection field for an object
Summarize the properties of an object
summary.GeneralSubstitution
Summarize the properties of an object
Set the rate parameters
Summarize the properties of an object
Set the rate parameters
Specify the list of Process objects attached to a Site object
Forbidden action: setting the unscaled rate matrix for a QMatrix object
Summarize the properties of an object
summary.ToleranceSubstitution
Summarize the properties of an object
Forbidden action: setting the node identifiers for a PhyloSim object
Assotiate a process object with a QMatrix object
Specify a set of Process objects to be attached to a set of Site objects aggregated by a Sequence object
Forbidden action: setting the type of a FastFieldDeletor object
Forbidden action: setting the string representation of a Sequence object
setScale.BrownianInsertor
Set scale parameter
Forbidden action: setting the length of a Sequence object
Set the deletion length probabilities
Forbidden action: setting the tree length for a PhyloSim object
Set an unscaled rate in a QMatrix object
Set the value of a rate parameter
Summarize the properties of an object
Set the name of a QMatrix object
Set an unscaled rate for an event from a GY94 object
setUniqueAlphabets.Sequence
Forbidden action: setting the list of unique Alphabet objects attached to the Site object aggregated by a Sequence object
setRate.GeneralSubstitution
Set an unscaled rate for an event from a GeneralSubstitution object
Set the name of a Sequence object
Summarize the properties of an object
Summarize the properties of an object
Set the value of a rate parameter
Summarize the properties of an object
Set the rate parameters
Summarize the properties of an object
Summarize the properties of an object
Set the rate parameters
setSizes.DiscreteInsertor
Set the sizes of the proposed insertions
Set the rate parameters
Set the state of a Site object
Forbidden action: setting the identifier of the root node for a PhyloSim object
Summarize the properties of an object
Summarize the properties of an object
setSiteSpecificParamIds.Process
Forbidden action: setting the paramter identifiers of the site specific paramters from a Process object
Forbidden action: setting the node identifiers of the tip nodes for a PhyloSim object
setToleranceMargin.FastFieldDeletor
Set the tolerance margin
Returns the string length of the character representation of an object
summary.ContinuousInsertor
Summarize the properties of an object
summary.ContinuousDeletor
Summarize the properties of an object
Returns the string lengths of the character represenations of a collection of objects
Summarize the properties of an object
Summarize the properties of an object
Summarize the properties of an object
setProbs.DiscreteInsertor
Set the insertion length probabilities
Set the rate parameters
setSiteSpecificParamList.Process
Forbidden action: setting the site specific paramter list for a Process object
Set Alphabet object type
Summarize the properties of an object
Forbidden action: setting the symbol set size of an Alphabet object
Set the sizes of the proposed deletions
Set the write protection field for an object
setWriteProtected.Process
Set the write protection field for an object
Set the general rate
Summarize the properties of an object
Forbidden action: getting the list of rate parameters
setRate.ToleranceSubstitution
Set an unscaled rate for an event from a ToleranceSubstitution object
Forbidden action: setting the type of a BrownianInsertor object
setRateList.GeneralSubstitution
Setting the rates for a GeneralSubstitution object
Summarize the properties of an object
Summarize the properties of an object
Summarize the properties of an object
Summarize the properties of an object
Set the value of a rate parameter
setWriteProtected.Alphabet
Set the write protection field for an object
translateCodon.CodonAlphabet
Translate a codon
Forbidden action: setting the scaled rate matrix for a QMatrix object
Summarize the properties of an object
Assotiate a Sequence object with a Site object
Forbidden action: setting the symbol length for an Alphabet object
Forbidden action: setting the list of total site rates for a Sequence object
Forbidden action: setting the total active event rate for a Site object
setUniqueProcesses.Sequence
Forbidden action: setting the list of unique Process instances attached to the sites of a Sequence object
Summarize the properties of an object
Summarize the properties of an object
Summarize the properties of an object
virtualAssignmentForbidden.PSRoot
Throws an error message informing the user about forbidden action on virtual a field
Summarize the properties of an object
Summarize the properties of an object