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phylosim (version 3.0.5)

Flexible Simulations of Biological Sequence Evolution

Description

An extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses Gillespie's direct method to simulate substitutions, insertions and deletions. Citation: Botond Sipos, Tim Massingham, Gregory E Jordan and Nick Goldman (2011) PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment .

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Install

install.packages('phylosim')

Monthly Downloads

123

Version

3.0.5

License

GPL (>= 3)

Issues

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Repository

https://github.com/bsipos/phylosim

Maintainer

Botond Sipos

Last Published

November 21st, 2019

Functions in phylosim (3.0.5)

The BinarySubst class

Check whether the two supplied Process objects are identical

The BinaryAlphabet class

The AnyAlphabet class

The Alphabet class

AminoAcidSequence

The AminoAcidSequence class

Check if two alaphabet objects have the same symbol set

The BinarySequence class

AminoAcidAlphabet

The AminoAcidAlphabet class

The AminoAcidSubst class

Save a debug message in the PhyloSim log file

The CodonSubst class

ContinuousDeletor

The ContinuousDeletor class

BrownianInsertor

The BrownianInsertor class

The ECMunrest empirical codon substitution model

ContinuousInsertor

The ContinuousInsertor class

The Event class

BrownianPath.BrownianInsertor

Generate a Brownian path

The CodonAlphabet class

The CodonSequence class

DiscreteInsertor

The DiscreteInsertor class

The ECMrest empirical codon substitution model

The LG empirical amino acid substitution model

The GeneralInDel class

The CodonUNREST class

FastFieldDeletor

The FastFieldDeletor class

DiscreteDeletor

The DiscreteDeletor 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 MtZoa empirical amino acid substitution model

Save a message in the PhyloSim log file

The GeneralDeletor class

The JTT empirical amino acid substitution model

NucleotideAlphabet

The NucleotideAlphabet class

GeneralSubstitution

The GeneralSubstitution class

GeneralInsertor

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 PhyloSim class

NucleotideSequence

The NucleotideSequence class

ToleranceSubstitution

The ToleranceSubstitution class

The Sequence class

Scale the scaled rate matrix stored in a QMatrix object by the provided factor

Simulate.PhyloSim

Run a simulation according to a PhyloSim object

areSynonymous.CodonAlphabet

Check whether two codons are synonymous

The UNREST class

checkConsistency.Alphabet

Check object consistency

checkConsistency.DiscreteDeletor

Check object consistency

as.character.Event

Get the character representation of an Event object

as.character.Alphabet

Get the character representation of an Alphabet object

checkConsistency.ContinuousInsertor

Check object consistency

buildFromPAML.CodonSubst

Build rate matrix from PAML file

Translate.CodonSequence

Translate a CodonSequence object

as.character.PhyloSim

Return the character representation of a PhyloSim object

as.character.GeneralSubstitution

Return the character representation of a GeneralSubstitution object

attachSeqToNode.PhyloSim

Assotiate a Sequence object with a given node of a phylo object aggregated by a PhyloSim 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

checkConsistency.CodonSequence

Check object consistency

checkConsistency.Event

Check object consistency

buildFromPAML.AminoAcidSubst

Build rate matrix from PAML file

checkConsistency.DiscreteInsertor

Check object consistency

checkConsistency.Process

Check object consistency

checkConsistency.AminoAcidSubst

Check object consistency

attachProcess.Sequence

Attach a Process object to a set of Site objects aggregated by a Sequence object

as.character.QMatrix

Return the character representation of a QMatrix object

as.character.Process

Get the character representation of a Process object

as.character.Sequence

Get the string representation of a Sequence object

as.character.Site

Get the character representation of a Site object

checkConsistency.BrownianInsertor

Check object consistency

Undocumented.PhyloSim

Undocumented object (PhyloSim package)

checkConsistency.CodonSubst

Check object consistency

checkConsistency.CodonAlphabet

Check object consistency

checkConsistency.QMatrix

Check object consistency

attachProcess.Site

Attach a Process object to a Site object

checkConsistency.CodonUNREST

Check object consistency

checkConsistency.GTR

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

checkConsistency.GY94

Check object consistency

checkConsistency.BinarySubst

Check object consistency

checkConsistency.JC69

Check object consistency

Clone a Sequence object

checkConsistency.GeneralSubstitution

Check object consistency

checkConsistency.TN93

Check object consistency

checkConsistency.K80

Check object consistency

checkConsistency.T92

Check object consistency

The cpREV empirical amino acid substitution model

checkConsistency.GeneralDeletor

Check object consistency

checkConsistency.HKY

Check object consistency

clone.ToleranceSubstitution

Clone a ToleranceSubstitution object

checkConsistency.F84

Check object consistency

checkConsistency.F81

Check object consistency

copySubSequence.Sequence

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

getAlphabet.QMatrix

Get the Alphabet object associated with a QMatrix object

generateInsert.GeneralInsertor

Generate an insert

flagTotalRate.Site

Flag the total event rate

checkConsistency.PSRootSummary

Check object consistency

clearStates.Sequence

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

exportStatTree.PhyloSim

Export the per-branch counts of an event as a phylo object

getAlphabet.Site

Get the Alphabet object attached to a Site object

enableVirtual.PSRoot

Enable the use of virtual fields for a given object

checkConsistency.ToleranceSubstitution

Check object consistency

checkConsistency.UNREST

Check object consistency

detachProcess.Site

getAlignment.PhyloSim

Get the alignment stored in a PhyloSim object

checkConsistency.K81

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

getAcceptBy.GeneralInDel

Get the function used for accepting/rejecting indel events

getAcceptWin.GeneralInsertor

Get the size of the acceptance window

getBaseFreqs.F81

Get the base frequency parameters

getBaseFreqs.GTR

Get the base frequency parameters

getCumulativeRatesFromRange.Sequence

Get the cumulative site rates for a collection of Site objects aggregated by a Sequence object

getBaseFreqs.HKY

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

getBaseFreqs.F84

Get the base frequency parameters

checkConsistency.PSRoot

Check object consistency

getBaseFreqs.K80

Get the base frequency parameters

getAlphabet.ToleranceSubstitution

Get the Alphabet object aggregated by a ToleranceSubstitution object

getCodonFreqs.GY94

Get codon frequencies

getBranchEvents.PhyloSim

Get the list of events having per-branch statistics recorded

getAlphabets.Sequence

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

getComments.PSRoot

Get the comments associated with an object

getBaseFreqs.K81

Get the base frequency parameters

checkConsistency.Sequence

Check object consistency

checkConsistency.Site

Check object consistency

getEvents.Sequence

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

getEdges.PhyloSim

Get the edge matrix from a phylo object aggregated by a PhyloSim object

getEdge.PhyloSim

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

detachProcess.Sequence

Detach a Process object from a set of Site objects aggregated by a Sequence object

getAncestral.Sequence

Get the ancestral object of a Sequence object

getBigRate.Sequence

Get the sum of all active event rates from a Sequence object

getBaseFreqs.TN93

Get the base frequency parameters

getAncestral.Site

Get the ancestral object of a Site object

getAlphabet.Process

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

getEventRate.QMatrix

Get the unscaled rate of an event from a QMatrix object

getEventsAtSite.GY94

Generate the list of active Event objects for a given attached Site object

getEventsAtSite.GeneralDeletor

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

getMethodsList.PSRoot

Get the list of applicable methods for an object

getEventsAtSite.FastFieldDeletor

Generate a deletion event object given the state of the target site

getLogFile.PhyloSim

Get the name of the file used for logging

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

getLengthParam1.FastFieldDeletor

Get the first length parameter

getEquDist.GeneralSubstitution

Get the equilibrium distribution from a GeneralSubstitution object

getLength.Sequence

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

getHandler.Event

Get the handler function of an Event object

getProcesses.Sequence

Get the Process objects attached to the Site objects aggregated by a Sequence object

getName.PhyloSim

Get the name of a PhyloSim object

getName.Process

Get the name of a Process 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

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

getEventsAtSite.Process

Generate the list of active Event objects given a Site object

getProcess.QMatrix

Get the process object associated with a QMatrix object

getMaxLength.ContinuousDeletor

Get the maximum length

getPhylo.PhyloSim

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

getRateParam.F84

Get the value of a rate parameter

getProcesses.Site

Get the list of Process objects attached to a Site object

getLogLevel.PhyloSim

Get the log level from a PhyloSim object

getPosition.Event

Get the position of the Site object associated to an Event object in the enclosing Sequence object

getSeqFromNode.PhyloSim

Get the Sequence object associated with a given node of a phylo object aggregated by a PhyloSim object

getName.QMatrix

Get the name of a QMatrix object

getMatrix.QMatrix

Get the unscaled rate matrix form a QMatrix object

getName.Sequence

Get the name of a Sequence object

Get the rate of an Event object

getRateParam.GTR

Get the value of a rate parameter

getSizes.DiscreteDeletor

Get the sizes of the proposed deletions

getProbs.DiscreteDeletor

Get the deletion length probabilities

getRate.GeneralInDel

Get the general rate

getTipLabels.PhyloSim

Get the tip labels from a phylo object aggregated by a PhyloSim object

getProposeBy.GeneralInDel

Get the function used for proposing indel lengths

getProcess.Event

Get the Process object which generated an Event object

getProbs.DiscreteInsertor

Get the insertion length probabilities

getRootSeq.PhyloSim

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

getRate.QMatrix

Get an unscaled rate of an event from a QMatrix object

getRateParamList.F81

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

getStates.Sequence

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

getRateParam.TN93

Get the value of a rate parameter

getType.Alphabet

Get Alphabet obejct type

getSize.Alphabet

Get the number of symbols in an Alphabet object

globalConsistencyCheck.PSRoot

Check the consistency of all objects inheriting form PSRoot in the current environment

getType.BrownianInsertor

Get the type of the BrownianInsertor process

getRateParamList.GTR

Get the rate parameters

getTemplateSeq.GeneralInsertor

Get the template sequence object

getScaledMatrix.QMatrix

Get the scaled rate matrix form a QMatrix object

Get the GC content

getRateList.QMatrix

Get a list of events and their unscaled rates from a QMatrix object

getSymbolLength.Alphabet

Get the length of the symbols in a given alphabet object

getRateParamList.F84

Get the rate parameters

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

hasSiteSpecificParameter.Process

Check if a Process object has the site-process specific parameter with the given id

is.tip.PhyloSim

Check if a node is a tip

getTips.PhyloSim

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

getRootNode.PhyloSim

Get the identifier of the root node from a PhyloSim object

getRateParamList.TN93

Get the rate parameters

getTotalRates.Sequence

Get the total site rates from a Sequence object

getRateParam.F81

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

is.GeneralInDel

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

getString.Sequence

Get the string representation of a Sequence object

getRateParamList.HKY

Get the rate parameters

getRateParam.K80

Get the value of a rate parameter

getRateParam.HKY

Get the value of a rate parameter

intersect.list.PSRoot

Utility method returning the intersection of two lists

hasSymbols.Alphabet

Check if an Alphabet object has a given set of symbols

getType.FastFieldDeletor

Get the type of a FastFieldDeletor object

getRateParam.K81

Get the value of a rate parameter

getRateParam.T92

Get the value of a rate parameter

getSequence.Site

Get the Sequence object associated with a given Site object

getWriteProtected.Sequence

Check if the object is write protected

getRateParamList.K80

Get the rate parameters

getTransTable.CodonAlphabet

Get the list storing the genetic code table

is.GeneralDeletor

Check whether an object inherits from GeneralDeletor

Check whether an object inherits from CodonUNREST

is.CodonAlphabet

Check if an object inherits from CodonAlphabet

getSymbolFreqs.Sequence

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

getTableId.CodonAlphabet

Get the genetic code id

getToleranceMargin.FastFieldDeletor

Get the tolerance margin

plot.ContinuousDeletor

Plot the density of proposed lengths

getSymbols.Alphabet

Get the symbol set from an Alphabet object

isAttached.Site

Check whether a Process object is attached to a Site object

omegaVarM0.CodonSequence

The M0 (one-ratio) model of variable omega ratios among sites

getRateParamList.K81

Get the rate parameters

omegaHist.CodonSequence

Plot a histogram of omega values from a range

getRateParamList.T92

Get the rate parameters

getTotalRate.Site

Get the total active event rate

is.GeneralInsertor

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

getSequences.PhyloSim

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

getTreeLength.PhyloSim

Get the tree length from a PhyloSim object

getWriteProtected.Event

Check if the object is write protected

getWriteProtected.Process

Check if the object is write protected

insertSequence.Sequence

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

is.GeneralSubstitution

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

is.ToleranceSubstitution

Check if an object is an instance of the ToleranceSubstitution class

readAlignment.PhyloSim

Read alignment from file

The mtArt empirical amino acid substitution model

sampleStates.Sequence

Sample the states for a collection of Site objects aggregated by a Sequence object

hasUndefinedRate.Process

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

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

getWriteProtected.Alphabet

Check if the object is write protected

isStopCodon.CodonAlphabet

Check if a codon is a stop codon

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

readTree.PhyloSim

Read tree from file

my.all.equal.PSRoot

Test if two objects are nearly equal

plot.ContinuousInsertor

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.PSRootSummary

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

omegaVarM3.CodonSequence

The M3 (discrete) model of variable omega ratios among sites

setAcceptBy.GeneralInDel

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

setBaseFreqs.HKY

Set the base frequency parameters

sampleState.ToleranceSubstitution

Sample a state from the equlibrium distribution of a ToleranceSubstitution object

setBaseFreqs.K80

Forbidden action: setting the base frequency parameters for a K80 object

setAncestral.Site

Forbidden action: setting the ancestral object for a Site object

plot.DiscreteDeletor

Plot the deletion length distribution

omegaVarM4.CodonSequence

The M4 (freqs) model of variable omega ratios among sites

plot.DiscreteInsertor

Plot the insertion length distribution

newAAMatrix.AminoAcidSubst

Undocumented method

isEmpty.Alphabet

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

setEdges.PhyloSim

Forbidden action: setting the edge matrix for a phylo object aggregated by a PhyloSim object

setName.Process

Set the name of a Process object

setCumulativeRates.Sequence

Forbidden action: setting the cumulative rates for the sites aggregated by a Sequence object

plot.GeneralSubstitution

Create a bubble plot of the substitution process

setBaseFreqs.F81

Set the base frequency parameters

newMatrix.CodonSubst

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

omegaVarM1.CodonSequence

The M1 (neutral) model of variable omega ratios among sites

omegaVarM2.CodonSequence

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

setName.PhyloSim

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

setLogFile.PhyloSim

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

setAlphabet.Process

Assotiate an Alphabet object with a Process object

proposeLength.GeneralInDel

Propose indel length

setBaseFreqs.F84

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

saveAlignment.PhyloSim

Save the alignment stored in a PhyloSim object in a Fasta file

setQMatrix.ToleranceSubstitution

Set the QMatrix object aggregated by a ToleranceSubstitution object

setOmegas.CodonSequence

Set the omegas for a collection of sites

setNtips.PhyloSim

Forbidden action: setting the number of the tips for a phylo object aggregated by a PhyloSim object

setAlphabet.QMatrix

Set the Alphabet object for a QMatrix object

setStates.Sequence

Set the states for a set of Site objects aggregated by a Sequence object

setInsertHook.GeneralInsertor

Set the insert hook function

setSequences.PhyloSim

Forbidden action: setting the Sequence objects associated with the nodes of a phylo object aggregated by a PhyloSim object

setPhylo.PhyloSim

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

setRateParam.F81

Forbidden action: getting the list of rate parameters

setTableId.CodonAlphabet

Forbidden action: setting the genetic code id

setRootSeq.PhyloSim

Set the root sequence for a PhyloSim object

setAlphabet.Site

Attach an Alphabet object to a Site object

scaleTree.PhyloSim

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

setCodonFreqs.GY94

Get codon frequencies

setAlignment.PhyloSim

Forbidden action: setting the alignment stored in a PhyloSim object

setAlphabet.GeneralSubstitution

Set the Alphabet object aggregated by a GeneralSubstitution object

setSymbols.Alphabet

Specify a new symbol set for an Alphabet object

setBaseFreqs.TN93

Set the base frequency parameters

setBaseFreqs.K81

Forbidden action: setting the base frequency parameters for a K81 model

setNedges.PhyloSim

Forbidden action: setting the number of edges for phylo object aggregated by a PhyloSim object

setBigRate.Sequence

Forbidden action: setting the sum of total active event rates for a Sequence object

setEquDist.ToleranceSubstitution

Set the equilibrium distribution for a ToleranceSubstitution object

setBaseFreqs.GTR

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

setLogLevel.PhyloSim

Set the log level for a given PhyloSim object

setBranchEvents.PhyloSim

Forbidden action: setting the list of events having per-branch statistics recorded

setAlphabets.Sequence

Assotiate Alphabet objects to a set of Site objects aggregated by a Sequence object

setComments.PSRoot

Set the comments associated with an object

setRateParam.K81

Set the value of a rate parameter

setHandler.Event

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

setAncestral.Sequence

Set the ancestral object of a Sequence object

setRateParam.T92

Set the value of a rate parameter

setRateParam.F84

Set the value of a rate parameter

setLengthParam1.FastFieldDeletor

Set the first length parameter

Forbidden action: setting the unique Process object identifier

setProcess.Event

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

setPosition.Event

Set the position of the Site object associated to an Event object

setMethodsList.PSRoot

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

setRateParam.GTR

Set the value of a rate parameter

summary.Alphabet

Summarize the properties of an object

setRateList.QMatrix

Setting the unscaled rates stored in a QMatrix object

setTemplateSeq.GeneralInsertor

Set the template sequence object

summary.BinarySubst

Summarize the properties of an object

summary.BrownianInsertor

Summarize the properties of an object

Set the GC content

setTipLabels.PhyloSim

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

setRateParamList.K81

Set the rate parameters

summary.GeneralInsertor

Summarize the properties of an object

setWriteProtected.Sequence

Set the write protection field for an object

summary.Process

Summarize the properties of an object

summary.GeneralSubstitution

Summarize the properties of an object

setRateParamList.T92

Set the rate parameters

summary.QMatrix

Summarize the properties of an object

setRateParamList.HKY

Set the rate parameters

setProcesses.Site

Specify the list of Process objects attached to a Site object

setMatrix.QMatrix

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

setNodes.PhyloSim

Forbidden action: setting the node identifiers for a PhyloSim 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

setType.FastFieldDeletor

Forbidden action: setting the type of a FastFieldDeletor object

setString.Sequence

Forbidden action: setting the string representation of a Sequence object

setScale.BrownianInsertor

Set scale parameter

setLength.Sequence

Forbidden action: setting the length of a Sequence object

setProbs.DiscreteDeletor

Set the deletion length probabilities

setTreeLength.PhyloSim

Forbidden action: setting the tree length for a PhyloSim object

setRate.QMatrix

Set an unscaled rate in a QMatrix object

setRateParam.K80

Set the value of a rate parameter

Summarize the properties of an object

setName.QMatrix

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

setName.Sequence

Set the name of a Sequence object

summary.AminoAcidSubst

Summarize the properties of an object

summary.FastFieldDeletor

Summarize the properties of an object

setRateParam.HKY

Set the value of a rate parameter

Summarize the properties of an object

setRateParamList.TN93

Set the rate parameters

Summarize the properties of an object

Summarize the properties of an object

setRateParamList.GTR

Set the rate parameters

setSizes.DiscreteInsertor

Set the sizes of the proposed insertions

setRateParamList.F84

Set the rate parameters

Set the state of a Site object

setRootNode.PhyloSim

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

setTips.PhyloSim

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

stringLengthVector

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

setRateParamList.K80

Set the rate parameters

setSiteSpecificParamList.Process

Forbidden action: setting the site specific paramter list for a Process object

setType.Alphabet

Set Alphabet object type

summary.DiscreteDeletor

Summarize the properties of an object

setSize.Alphabet

Forbidden action: setting the symbol set size of an Alphabet object

setSizes.DiscreteDeletor

Set the sizes of the proposed deletions

setWriteProtected.Event

Set the write protection field for an object

setWriteProtected.Process

Set the write protection field for an object

setRate.GeneralInDel

Set the general rate

summary.GeneralDeletor

Summarize the properties of an object

setRateParamList.F81

Forbidden action: getting the list of rate parameters

setRate.ToleranceSubstitution

Set an unscaled rate for an event from a ToleranceSubstitution object

setType.BrownianInsertor

Forbidden action: setting the type of a BrownianInsertor object

setRateList.GeneralSubstitution

Setting the rates for a GeneralSubstitution object

summary.DiscreteInsertor

Summarize the properties of an object

Summarize the properties of an object

summary.GeneralInDel

Summarize the properties of an object

summary.PhyloSim

Summarize the properties of an object

setRateParam.TN93

Set the value of a rate parameter

setWriteProtected.Alphabet

Set the write protection field for an object

translateCodon.CodonAlphabet

Translate a codon

setScaledMatrix.QMatrix

Forbidden action: setting the scaled rate matrix for a QMatrix object

summary.CodonAlphabet

Summarize the properties of an object

setSequence.Site

Assotiate a Sequence object with a Site object

setSymbolLength.Alphabet

Forbidden action: setting the symbol length for an Alphabet object

setTotalRates.Sequence

Forbidden action: setting the list of total site rates for a Sequence object

setTotalRate.Site

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

summary.Sequence

Summarize the properties of an object

summary.CodonSubst

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