Man pages for phylosim
Flexible Simulations of Biological Sequence Evolution
| 000==.Alphabet | Check if two alaphabet objects have the same symbol set |
| 000==.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 |
| 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... |
| 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... |
| attachHookToNode.PhyloSim | Attach a callback function to a given node of a phylo object... |
| attachProcess.Sequence | Attach a Process object to a set of Site objects aggregated... |
| attachProcess.Site | Attach a Process object to a Site object |
| attachSeqToNode.PhyloSim | Assotiate a Sequence object with a given node of a phylo... |
| BinaryAlphabet | The BinaryAlphabet class |
| BinarySequence | The BinarySequence class |
| BinarySubst | The BinarySubst class |
| BrownianInsertor | The BrownianInsertor class |
| BrownianPath.BrownianInsertor | Generate a Brownian path |
| 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.GeneralDeletor | Check object consistency |
| checkConsistency.GeneralInDel | Check object consistency |
| checkConsistency.GeneralInsertor | Check object consistency |
| checkConsistency.GeneralSubstitution | Check object consistency |
| checkConsistency.GTR | Check object consistency |
| checkConsistency.GY94 | Check object consistency |
| checkConsistency.HKY | Check object consistency |
| checkConsistency.JC69 | Check object consistency |
| checkConsistency.K80 | Check object consistency |
| checkConsistency.K81 | Check object consistency |
| checkConsistency.PhyloSim | Check object consistency |
| checkConsistency.Process | Check object consistency |
| checkConsistency.PSRoot | Check object consistency |
| checkConsistency.PSRootSummary | 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... |
| clone.GeneralSubstitution | Clone a GeneralSubstitution object |
| clone.Process | Clone a process object |
| clone.Sequence | Clone a Sequence object |
| clone.ToleranceSubstitution | Clone a ToleranceSubstitution object |
| CodonAlphabet | The CodonAlphabet class |
| CodonSequence | The CodonSequence class |
| CodonSubst | The CodonSubst class |
| CodonUNREST | The CodonUNREST class |
| ContinuousDeletor | The ContinuousDeletor class |
| ContinuousInsertor | The ContinuousInsertor class |
| copySubSequence.Sequence | Copy a collection of Site objects aggregated by a Sequence... |
| cpREV | The cpREV empirical amino acid substitution model |
| Debug.PhyloSim | Save a debug message in the PhyloSim log file |
| 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... |
| detachProcess.Sequence | Detach a Process object from a set of Site objects aggregated... |
| detachProcess.Site | Site |
| detachSeqFromNode.PhyloSim | Detach a Sequence object from a given node of a phylo object... |
| DiscreteDeletor | The DiscreteDeletor class |
| DiscreteInsertor | The DiscreteInsertor class |
| ECMrest | The ECMrest empirical codon substitution model |
| ECMunrest | The ECMunrest empirical codon substitution model |
| enableVirtual.PSRoot | Enable the use of virtual fields for a given object |
| Event | The Event class |
| exportStatTree.PhyloSim | Export the per-branch counts of an event as a phylo object |
| F81 | The F81 class |
| F84 | The F84 class |
| FastFieldDeletor | The FastFieldDeletor class |
| flagTotalRate.Site | Flag the total event rate |
| GeneralDeletor | The GeneralDeletor class |
| GeneralInDel | The GeneralInDel class |
| GeneralInsertor | The GeneralInsertor class |
| GeneralSubstitution | The GeneralSubstitution class |
| 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 |
| getAlignmentLength.PhyloSim | Get the alignment length from a PhyloSim object |
| getAlignment.PhyloSim | Get the alignment stored in a PhyloSim object |
| getAlphabet.GeneralSubstitution | Get the Alphabet object aggregated by a GeneralSubstitution... |
| getAlphabet.Process | Get the Alphabet object associated with a given Process... |
| getAlphabet.QMatrix | Get the Alphabet object associated with a QMatrix object |
| getAlphabet.Site | Get the Alphabet object attached to a Site object |
| getAlphabets.Sequence | Get the list of the Alphabet objects attached to the Site... |
| getAlphabet.ToleranceSubstitution | Get the Alphabet object aggregated by a ToleranceSubstitution... |
| 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 |
| getCumulativeRatesFromRange.Sequence | Get the cumulative site rates for a collection of Site... |
| getCumulativeRates.Sequence | Get the total site rates from a Sequence object |
| getDeletionTolerance.Sequence | Get the deletion tolerance site-process specific parameter... |
| 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... |
| getEquDist.GeneralSubstitution | Get the equilibrium distribution from a GeneralSubstitution... |
| getEquDist.ToleranceSubstitution | Get the equilibrium distribution from a ToleranceSubstitution... |
| getEventRateAtSite.GeneralSubstitution | Get the site spcific rate of an event from a... |
| getEventRateAtSite.ToleranceSubstitution | Get the site spcific rate of an event from a... |
| getEventRate.GeneralSubstitution | Get the scaled rate of an event from a GeneralSubstitution... |
| 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... |
| getEventsAtSite.FastFieldDeletor | Generate a deletion event object given the state of the... |
| getEventsAtSite.GeneralDeletor | Title |
| getEventsAtSite.GeneralInsertor | Generate insertion event object given the state of the target... |
| getEventsAtSite.GeneralSubstitution | Generate the list of active Event objects for a given... |
| getEventsAtSite.GY94 | Generate the list of active Event objects for a given... |
| 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... |
| getEvents.Sequence | Get the list of active Event objects for a set of Site... |
| getEvents.Site | Get the list of active event objects given the current state... |
| 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... |
| getKappa.F84 | Get the transition transversion rate ratio |
| getKappa.GY94 | Get the transition/transversion rate ratio |
| getLengthParam1.FastFieldDeletor | Get the first length parameter |
| getLengthParam2.FastFieldDeletor | Get the second length parameter |
| getLength.Sequence | Get the number of Site objects aggregated in a Sequence... |
| 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... |
| getNodes.PhyloSim | Get the node identifiers from a PhyloSim object |
| getNtips.PhyloSim | Get the number of the tips form a phylo object aggregated by... |
| 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... |
| getParameterAtSites.Sequence | Get the values of a site-process specific paramater for a... |
| getPhylo.PhyloSim | Get the phylo object aggregated in a PhyloSim object |
| getPosition.Event | Get the position of the Site object associated to an Event... |
| getProbs.DiscreteDeletor | Get the deletion length probabilities |
| getProbs.DiscreteInsertor | Get the insertion length probabilities |
| getProcesses.Sequence | Get the Process objects attached to the Site objects... |
| getProcesses.Site | Get the list of Process objects attached to a Site object |
| getProcess.Event | Get the Process object which generated an Event object |
| getProcess.QMatrix | Get the process object associated with a QMatrix object |
| getProposeBy.GeneralInDel | Get the function used for proposing indel lengths |
| getQMatrix.GeneralSubstitution | Get the QMatrix object aggregated by a GeneralSubstitution... |
| getQMatrix.ToleranceSubstitution | Get the QMatrix object aggregated by a ToleranceSubstitution... |
| 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... |
| getRateList.GeneralSubstitution | Get a list of events and their unscaled rates from a... |
| getRateList.QMatrix | Get a list of events and their unscaled rates from a QMatrix... |
| getRateList.ToleranceSubstitution | Get a list of events and their unscaled rates from a... |
| getRateMultipliers.Sequence | Get the values of the rate multiplier parameters for a given... |
| 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 |
| 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 |
| getRateParam.T92 | Get the value of a rate parameter |
| getRateParam.TN93 | Get the value of a rate parameter |
| 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... |
| 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... |
| 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... |
| getSite.Event | Get the Site object associated with an Event object |
| getSiteSpecificParamIds.Process | Get the site specific paramter identifiers from a Process... |
| 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... |
| 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... |
| getString.Sequence | Get the string representation of a Sequence object |
| getSymbolFreqs.Sequence | Get a table with the frequencies of the states of a... |
| 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... |
| getTips.PhyloSim | Get the node identifiers of the tip nodes from a PhyloSim... |
| getToleranceMargin.FastFieldDeletor | Get the tolerance margin |
| getTotalRatesFromRange.Sequence | Get the vector of total site rates for a collection of Site... |
| getTotalRate.Site | Get the total active event rate |
| getTotalRates.Sequence | Get the total site rates from 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... |
| getUniqueProcesses.Sequence | Get the list of unique Process instances attached to the Site... |
| 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... |
| GTR | The GTR class |
| GY94 | The GY94 class |
| hasSiteSpecificParameter.Process | Check if a Process object has the site-process specific... |
| 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... |
| 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 |
| HKY | The HKY class |
| insertSequence.Sequence | Insert a Sequence object into another Sequence object after a... |
| intersect.list.PSRoot | Utility method returning the intersection of two lists |
| is.Alphabet | Check if an object is an instance of the Alphabet class |
| isAttached.Site | Check whether a Process object is attached to a Site object |
| is.CodonAlphabet | Check if an object inherits from CodonAlphabet |
| is.CodonUNREST | Check whether an object inherits from CodonUNREST |
| isEmpty.Alphabet | Check if the symbol set is empty |
| is.Event | Check whether an object inherits from the class Event |
| 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... |
| is.GY94 | Check whether an object inherits from GY94 |
| is.na.PSRoot | Check if a PSRoot object is NA |
| is.phylo | Check if an object is an instance of the phylo class |
| is.Process | Check if an object is an instance of the Process class |
| is.PSRoot | Check if an object inherits from PSRoot |
| 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 |
| isStartCodon.CodonAlphabet | Check if a codon is a start codon |
| isStopCodon.CodonAlphabet | Check if a codon is a stop codon |
| is.tip.PhyloSim | Check if a node is a tip |
| is.ToleranceSubstitution | Check if an object is an instance of the... |
| 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 |
| ll.PSRoot | Display detailed information about the virtual fields and... |
| Log.PhyloSim | Save a message in the PhyloSim log file |
| mtArt | The mtArt empirical amino acid substitution model |
| mtMam | The mtMam empirical amino acid substitution model |
| mtREV24 | The mtREV24 empirical amino acid substitution model |
| MtZoa | The MtZoa 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 |
| NucleotideAlphabet | The NucleotideAlphabet class |
| NucleotideSequence | The NucleotideSequence class |
| 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 |
| PAM | The PAM empirical amino acid substitution model |
| PAM.dcmut | The PAM.dcmut empirical amino acid substitution model |
| Perform.Event | Perform an event |
| PhyloSim | The PhyloSim class |
| 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 |
| plotParametersAtSites.Sequence | Plot the value of a site-process specifc paramter for a... |
| plot.PhyloSim | Plot a PhyloSim object |
| plot.Sequence | Plot the total site rates for a collection of Site objects... |
| plot.ToleranceSubstitution | Create a bubble plot of the substitution process |
| plusGamma.Sequence | Sample the rate multiplier parameters of a Process from a... |
| plusInvGamma.Sequence | Sample the rate multiplier parameters of a Process from an... |
| print.PSRootSummary | Print out a PSRootSummary object |
| print.QMatrix | Print the character representation of a QMatrix object |
| Process | The Process class |
| proposeLength.GeneralInDel | Propose indel length |
| PSRoot | The root class for all phylosim objects |
| PSRootSummary | The PSRootSummary class |
| QMatrix | The QMatrix class |
| readAlignment.PhyloSim | Read alignment from file |
| readTree.PhyloSim | Read tree from file |
| rescaleQMatrix.GeneralSubstitution | Rescale the scaled rate matrix of a QMatrix object aggregated... |
| rescaleQMatrix.ToleranceSubstitution | Rescale the scaled rate matrix of a QMatrix object aggregated... |
| revComp.NucleotideSequence | Reverse complmenet a NucleotideSequence object |
| sampleState.GeneralSubstitution | Sample a state from the equlibrium distribution of a... |
| sampleStates.Sequence | Sample the states for a collection of Site objects aggregated... |
| sampleState.ToleranceSubstitution | Sample a state from the equlibrium distribution of a... |
| saveAlignment.PhyloSim | Save the alignment stored in a PhyloSim object in a Fasta... |
| Scale.QMatrix | Scale the scaled rate matrix stored in a QMatrix object by... |
| scaleTree.PhyloSim | Scale the branch lengths of a phylo object aggragted by a... |
| Sequence | The Sequence class |
| 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... |
| setAlphabet.GeneralSubstitution | Set the Alphabet object aggregated by a GeneralSubstitution... |
| 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 |
| setAlphabets.Sequence | Assotiate Alphabet objects to a set of Site objects... |
| setAlphabet.ToleranceSubstitution | Set the Alphabet object aggregated by a ToleranceSubstitution... |
| setAncestral.Sequence | Set the ancestral object of a Sequence object |
| setAncestral.Site | Forbidden action: setting the ancestral object for a Site... |
| 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... |
| setBaseFreqs.K81 | Forbidden action: setting the base frequency parameters for a... |
| setBaseFreqs.TN93 | Set the base frequency parameters |
| setBigRate.Sequence | Forbidden action: setting the sum of total active event rates... |
| setBranchEvents.PhyloSim | Forbidden action: setting the list of events having... |
| 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... |
| setDeletionTolerance.Sequence | Set the deletion tolerance site-process specific parameter... |
| 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... |
| setEquDist.GeneralSubstitution | Set the equilibrium distribution for a GeneralSubstitution... |
| setEquDist.ToleranceSubstitution | Set the equilibrium distribution for a ToleranceSubstitution... |
| setEvents.Site | Forbidden action: setting the list of active events for a... |
| setGenerateBy.GeneralInsertor | Set the function object used for generating inserts |
| setHandler.Event | Forbidden action: setting the handler function of an Event... |
| setId.PhyloSim | Forbidden action: setting the unique identifier of a PhyloSim... |
| setId.Process | Forbidden action: setting the unique Process object... |
| setId.QMatrix | Forbidden action: setting the unique identifier for a QMatrix... |
| setId.Sequence | Forbidden action: setting the unique identifier of a Sequence... |
| setInsertHook.GeneralInsertor | Set the insert hook function |
| setInsertionTolerance.Sequence | Set the insertion tolerance site-process specific parameter... |
| setKappa.F84 | Get the transition transversion rate ratio |
| setKappa.GY94 | Set the transition/transversion rate ratio |
| setLengthParam1.FastFieldDeletor | Set the first length parameter |
| setLengthParam2.FastFieldDeletor | Set the second length parameter |
| setLength.Sequence | Forbidden action: setting the length of a Sequence object |
| 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... |
| setMaxLength.ContinuousDeletor | Set the maximum length |
| setMaxLength.ContinuousInsertor | Set the maximum length |
| setMethodsList.PSRoot | Forbidden action: setting the list of applicable methods for... |
| 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... |
| setNodes.PhyloSim | Forbidden action: setting the node identifiers for a PhyloSim... |
| setNtips.PhyloSim | Forbidden action: setting the number of the tips for a phylo... |
| setOmegas.CodonSequence | Set the omegas for a collection of sites |
| setParameterAtSite.Process | Set the value of a site-process specific paramter in a Site... |
| setParameterAtSites.Sequence | Set the values of a site-process specific paramater for a... |
| setPhylo.PhyloSim | Set the phylo object for a PhyloSim object |
| setPosition.Event | Set the position of the Site object associated to an Event... |
| setProbs.DiscreteDeletor | Set the deletion length probabilities |
| setProbs.DiscreteInsertor | Set the insertion length probabilities |
| setProcesses.Sequence | Specify a set of Process objects to be attached to a set of... |
| setProcesses.Site | Specify the list of Process objects attached to a Site object |
| setProcess.Event | Set the generator process for an Event object |
| setProcess.QMatrix | Assotiate a process object with a QMatrix object |
| setProposeBy.GeneralInDel | Set the function used for proposing indel lengths |
| setQMatrix.GeneralSubstitution | Set the QMatrix object aggregated by a GeneralSubstitution... |
| setQMatrix.ToleranceSubstitution | Set the QMatrix object aggregated by a ToleranceSubstitution... |
| setRate.Event | Set the rate of an Event object |
| setRate.GeneralInDel | Set the general rate |
| setRate.GeneralSubstitution | Set an unscaled rate for an event from a GeneralSubstitution... |
| setRate.GY94 | Set an unscaled rate for an event from a GY94 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... |
| 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 |
| 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 |
| setRateParam.T92 | Set the value of a rate parameter |
| setRateParam.TN93 | Set the value of a rate parameter |
| setRate.QMatrix | Set an unscaled rate in a QMatrix object |
| setRate.ToleranceSubstitution | Set an unscaled rate for an event from a... |
| setRootNode.PhyloSim | Forbidden action: setting the identifier of the root node for... |
| 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... |
| setSequence.Site | Assotiate a Sequence object with a Site object |
| setSequences.PhyloSim | Forbidden action: setting the Sequence objects associated... |
| setSite.Event | Assotiate an Event object with a Site object |
| setSiteSpecificParamIds.Process | Forbidden action: setting the paramter identifiers of the... |
| setSiteSpecificParamList.Process | Forbidden action: setting the site specific paramter list for... |
| setSize.Alphabet | Forbidden action: setting the symbol set size of an Alphabet... |
| 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... |
| setString.Sequence | Forbidden action: setting the string representation of a... |
| setSymbolLength.Alphabet | Forbidden action: setting the symbol length for an Alphabet... |
| 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... |
| setTips.PhyloSim | Forbidden action: setting the node identifiers of the tip... |
| setToleranceMargin.FastFieldDeletor | Set the tolerance margin |
| setTotalRate.Site | Forbidden action: setting the total active event rate for a... |
| setTotalRates.Sequence | Forbidden action: setting the list of total site rates for a... |
| setTransTable.CodonAlphabet | Forbidden action: setting the genetic code table for a... |
| setTreeLength.PhyloSim | Forbidden action: setting the tree length for a PhyloSim... |
| setType.Alphabet | Set Alphabet object type |
| setType.BrownianInsertor | Forbidden action: setting the type of a BrownianInsertor... |
| setType.FastFieldDeletor | Forbidden action: setting the type of a FastFieldDeletor... |
| setUniqueAlphabets.Sequence | Forbidden action: setting the list of unique Alphabet objects... |
| setUniqueProcesses.Sequence | Forbidden action: setting the list of unique Process... |
| 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 |
| Simulate.PhyloSim | Run a simulation according to a PhyloSim object |
| Site | The Site class |
| stringLength | Returns the string length of the character representation of... |
| stringLengthVector | Returns the string lengths of the character represenations of... |
| 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.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.GTR | Summarize the properties of an object |
| summary.GY94 | 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.PhyloSim | Summarize the properties of an object |
| summary.Process | Summarize the properties of an object |
| summary.PSRoot | 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 |
| T92 | The T92 class |
| TN93 | The TN93 class |
| ToleranceSubstitution | The ToleranceSubstitution class |
| translateCodon.CodonAlphabet | Translate a codon |
| Translate.CodonSequence | Translate a CodonSequence object |
| Undocumented.PhyloSim | Undocumented object (PhyloSim package) |
| UNREST | The UNREST class |
| virtualAssignmentForbidden.PSRoot | Throws an error message informing the user about forbidden... |
| WAG | The WAG empirical amino acid substitution model |
