phylosim: Flexible Simulations of Biological Sequence Evolution

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.

AuthorBotond Sipos <sbotond@gmail.com>, Gregory Jordan <greg@ebi.ac.uk>
Date of publication2016-09-08 20:14:57
MaintainerBotond Sipos <sbotond@gmail.com>
LicenseGPL (>= 3)
Version3.0.2
https://github.com/bsipos/phylosim

View on CRAN

Man pages

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

Files in this package

phylosim
phylosim/inst
phylosim/inst/extdata
phylosim/inst/extdata/MtZoa.dat
phylosim/inst/extdata/wag.dat
phylosim/inst/extdata/g1974a.dat
phylosim/inst/extdata/miyata.dat
phylosim/inst/extdata/ECMunrest.dat
phylosim/inst/extdata/mtArt.dat
phylosim/inst/extdata/jones.dat
phylosim/inst/extdata/dayhoff.dat
phylosim/inst/extdata/mtREV24.dat
phylosim/inst/extdata/g1974c.dat
phylosim/inst/extdata/ECMrest.dat
phylosim/inst/extdata/g1974p.dat
phylosim/inst/extdata/cpREV.dat
phylosim/inst/extdata/g1974v.dat
phylosim/inst/extdata/mtmam.dat
phylosim/inst/extdata/lg.dat
phylosim/inst/extdata/dayhoff-dcmut.dat
phylosim/inst/extdata/grantham.dat
phylosim/inst/extdata/jones-dcmut.dat
phylosim/inst/doc
phylosim/inst/doc/PhyloSim.pdf
phylosim/inst/doc/PhyloSim.Rnw
phylosim/inst/doc/PhyloSim.R
phylosim/NAMESPACE
phylosim/data
phylosim/data/WAG.RData
phylosim/data/mtArt.RData
phylosim/data/JTT.dcmut.RData
phylosim/data/ECMrest.RData
phylosim/data/LG.RData
phylosim/data/PAM.dcmut.RData
phylosim/data/JTT.RData
phylosim/data/mtREV24.RData
phylosim/data/ECMunrest.RData
phylosim/data/MtZoa.RData
phylosim/data/cpREV.RData
phylosim/data/mtMam.RData
phylosim/data/PAM.RData
phylosim/R
phylosim/R/GeneralSubstitution.R phylosim/R/CodonSubst.R phylosim/R/DiscreteDeletor.R phylosim/R/DiscreteInsertor.R phylosim/R/ContinuousInsertor.R phylosim/R/FieldDeletor.R phylosim/R/BinarySubst.R phylosim/R/PopularAlphabets.R phylosim/R/GeneralInDel.R phylosim/R/Alphabet.R phylosim/R/Event.R phylosim/R/AminoAcidSubst.R phylosim/R/QMatrix.R phylosim/R/PSRoot.R phylosim/R/CodonAlphabet.R phylosim/R/Site.R phylosim/R/BrownianInsertor.R phylosim/R/PopularSequences.R phylosim/R/AminoAcidMatrices.R phylosim/R/CodonModels.R phylosim/R/NucleotideModels.R phylosim/R/Sequence.R phylosim/R/EmpiricalCodonMatrices.R phylosim/R/ContinuousDeletor.R phylosim/R/PhyloSimSource.R phylosim/R/PhyloSim.R phylosim/R/Process.R phylosim/R/ToleranceSubstitution.R
phylosim/vignettes
phylosim/vignettes/Makefile
phylosim/vignettes/PhyloSim.Rnw
phylosim/MD5
phylosim/build
phylosim/build/vignette.rds
phylosim/DESCRIPTION
phylosim/man
phylosim/man/hasUndefinedRate.GeneralInDel.Rd phylosim/man/summary.F84.Rd phylosim/man/omegaVarM0.CodonSequence.Rd phylosim/man/setBaseFreqs.GTR.Rd phylosim/man/setRateParam.F84.Rd phylosim/man/checkConsistency.K81.Rd phylosim/man/checkConsistency.Sequence.Rd phylosim/man/getName.Event.Rd phylosim/man/print.QMatrix.Rd phylosim/man/setRate.QMatrix.Rd phylosim/man/getTemplateSeq.GeneralInsertor.Rd phylosim/man/setTransTable.CodonAlphabet.Rd phylosim/man/BrownianInsertor.Rd phylosim/man/setAlphabet.Site.Rd phylosim/man/is.GeneralDeletor.Rd phylosim/man/buildFromPAML.AminoAcidSubst.Rd phylosim/man/summary.PSRoot.Rd phylosim/man/ContinuousInsertor.Rd phylosim/man/checkConsistency.BinarySubst.Rd phylosim/man/setAlphabet.ToleranceSubstitution.Rd phylosim/man/checkConsistency.ToleranceSubstitution.Rd phylosim/man/setRateParamList.GTR.Rd phylosim/man/summary.GTR.Rd phylosim/man/setProposeBy.GeneralInDel.Rd phylosim/man/insertSequence.Sequence.Rd phylosim/man/getHandler.Event.Rd phylosim/man/setRateList.ToleranceSubstitution.Rd phylosim/man/as.character.Process.Rd phylosim/man/setLengthParam2.FastFieldDeletor.Rd phylosim/man/BinarySubst.Rd phylosim/man/checkConsistency.ContinuousInsertor.Rd phylosim/man/getEventRateAtSite.GeneralSubstitution.Rd phylosim/man/summary.GeneralInsertor.Rd phylosim/man/checkConsistency.GeneralDeletor.Rd phylosim/man/setName.QMatrix.Rd phylosim/man/setRateList.GeneralSubstitution.Rd phylosim/man/setBaseFreqs.F84.Rd phylosim/man/getProposeBy.GeneralInDel.Rd phylosim/man/setName.Process.Rd phylosim/man/getInsertHook.GeneralInsertor.Rd phylosim/man/getOmegas.CodonSequence.Rd phylosim/man/getEquDist.GeneralSubstitution.Rd phylosim/man/newAAMatrix.AminoAcidSubst.Rd phylosim/man/hasUndefinedRate.Process.Rd phylosim/man/getType.FastFieldDeletor.Rd phylosim/man/setAcceptBy.GeneralInDel.Rd phylosim/man/getCumulativeRatesFromRange.Sequence.Rd phylosim/man/UNREST.Rd phylosim/man/is.tip.PhyloSim.Rd phylosim/man/setRate.GY94.Rd phylosim/man/getBranchEvents.PhyloSim.Rd phylosim/man/setAlignment.PhyloSim.Rd phylosim/man/getComments.PSRoot.Rd phylosim/man/setRate.GeneralInDel.Rd phylosim/man/CodonAlphabet.Rd phylosim/man/is.CodonUNREST.Rd phylosim/man/setMaxLength.ContinuousDeletor.Rd phylosim/man/cpREV.Rd phylosim/man/checkConsistency.GeneralInDel.Rd phylosim/man/clone.Process.Rd phylosim/man/setNtips.PhyloSim.Rd phylosim/man/checkConsistency.CodonSequence.Rd phylosim/man/setLength.Sequence.Rd phylosim/man/checkConsistency.BrownianInsertor.Rd phylosim/man/getType.BrownianInsertor.Rd phylosim/man/setWriteProtected.Process.Rd phylosim/man/setRateParam.HKY.Rd phylosim/man/getRateParamList.HKY.Rd phylosim/man/getBaseFreqs.TN93.Rd phylosim/man/JC69.Rd phylosim/man/getMaxLength.ContinuousInsertor.Rd phylosim/man/deleteSubSequence.Sequence.Rd phylosim/man/hasUndefinedRate.ToleranceSubstitution.Rd phylosim/man/flagTotalRate.Site.Rd phylosim/man/is.Event.Rd phylosim/man/checkConsistency.AminoAcidSubst.Rd phylosim/man/HKY.Rd phylosim/man/getEquDist.ToleranceSubstitution.Rd phylosim/man/getProcesses.Sequence.Rd phylosim/man/getDist.ContinuousDeletor.Rd phylosim/man/setType.BrownianInsertor.Rd phylosim/man/getAlphabet.QMatrix.Rd phylosim/man/BrownianPath.BrownianInsertor.Rd phylosim/man/ECMunrest.Rd phylosim/man/PhyloSim.Rd phylosim/man/setRootSeq.PhyloSim.Rd phylosim/man/checkConsistency.K80.Rd phylosim/man/getRate.GeneralInDel.Rd phylosim/man/PSRootSummary.Rd phylosim/man/getEvents.Sequence.Rd phylosim/man/checkConsistency.GY94.Rd phylosim/man/getRateList.GeneralSubstitution.Rd phylosim/man/getWriteProtected.Sequence.Rd phylosim/man/getSiteSpecificParamIds.Process.Rd phylosim/man/print.PSRootSummary.Rd phylosim/man/checkConsistency.DiscreteInsertor.Rd phylosim/man/setTips.PhyloSim.Rd phylosim/man/hasSiteSpecificParameter.Process.Rd phylosim/man/summary.CodonSubst.Rd phylosim/man/setBranchEvents.PhyloSim.Rd phylosim/man/getName.Process.Rd phylosim/man/setRateParam.T92.Rd phylosim/man/getTransTable.CodonAlphabet.Rd phylosim/man/detachSeqFromNode.PhyloSim.Rd phylosim/man/setType.Alphabet.Rd phylosim/man/checkConsistency.ContinuousDeletor.Rd phylosim/man/enableVirtual.PSRoot.Rd phylosim/man/checkConsistency.GTR.Rd phylosim/man/setDeletionTolerance.Sequence.Rd phylosim/man/setRateMultipliers.Sequence.Rd phylosim/man/setRateParam.K81.Rd phylosim/man/getParameterAtSite.Process.Rd phylosim/man/getRate.Event.Rd phylosim/man/setEdges.PhyloSim.Rd phylosim/man/getName.Sequence.Rd phylosim/man/setTemplateSeq.GeneralInsertor.Rd phylosim/man/setDist.ContinuousDeletor.Rd phylosim/man/plotParametersAtSites.Sequence.Rd phylosim/man/Perform.Event.Rd phylosim/man/getEdges.PhyloSim.Rd phylosim/man/getScale.BrownianInsertor.Rd phylosim/man/summary.Sequence.Rd phylosim/man/setParameterAtSite.Process.Rd phylosim/man/setWriteProtected.QMatrix.Rd phylosim/man/stringLength.Rd phylosim/man/clone.GeneralSubstitution.Rd phylosim/man/setRateParam.F81.Rd phylosim/man/summary.ContinuousDeletor.Rd phylosim/man/getSymbolFreqs.Sequence.Rd phylosim/man/getEventsAtSite.GeneralDeletor.Rd phylosim/man/setProbs.DiscreteInsertor.Rd phylosim/man/getDeletionTolerance.Sequence.Rd phylosim/man/getTipLabels.PhyloSim.Rd phylosim/man/summary.DiscreteDeletor.Rd phylosim/man/getAlphabet.Site.Rd phylosim/man/as.character.Alphabet.Rd phylosim/man/proposeLength.GeneralInDel.Rd phylosim/man/getGenerateBy.GeneralInsertor.Rd phylosim/man/QMatrix.Rd phylosim/man/buildFromPAML.CodonSubst.Rd phylosim/man/getAcceptBy.GeneralInDel.Rd phylosim/man/attachProcess.Site.Rd phylosim/man/getOmegaScalingFactor.GY94.Rd phylosim/man/getKappa.GY94.Rd phylosim/man/is.GeneralInsertor.Rd phylosim/man/getLogFile.PhyloSim.Rd phylosim/man/setAlphabet.Process.Rd phylosim/man/setRateParamList.K80.Rd phylosim/man/setType.FastFieldDeletor.Rd phylosim/man/setAlphabet.QMatrix.Rd phylosim/man/checkConsistency.T92.Rd phylosim/man/getToleranceMargin.FastFieldDeletor.Rd phylosim/man/summary.GeneralSubstitution.Rd phylosim/man/rescaleQMatrix.ToleranceSubstitution.Rd phylosim/man/Log.PhyloSim.Rd phylosim/man/setAncestral.Site.Rd phylosim/man/getRateList.QMatrix.Rd phylosim/man/as.character.ToleranceSubstitution.Rd phylosim/man/getEventsAtSite.ToleranceSubstitution.Rd phylosim/man/getKappa.F84.Rd phylosim/man/setPosition.Event.Rd phylosim/man/getSymbolLength.Alphabet.Rd phylosim/man/getAncestral.Sequence.Rd phylosim/man/getMatrix.QMatrix.Rd phylosim/man/setRateList.QMatrix.Rd phylosim/man/is.GeneralInDel.Rd phylosim/man/getEdge.PhyloSim.Rd phylosim/man/attachHookToNode.PhyloSim.Rd phylosim/man/summary.F81.Rd phylosim/man/summary.BrownianInsertor.Rd phylosim/man/setRateParamList.K81.Rd phylosim/man/as.character.QMatrix.Rd phylosim/man/hasSymbols.Alphabet.Rd phylosim/man/setAlphabet.GeneralSubstitution.Rd phylosim/man/setScaledMatrix.QMatrix.Rd phylosim/man/omegaVarM2.CodonSequence.Rd phylosim/man/getEventRateAtSite.ToleranceSubstitution.Rd phylosim/man/summary.DiscreteInsertor.Rd phylosim/man/setBaseFreqs.K81.Rd phylosim/man/summary.HKY.Rd phylosim/man/getRateParamList.TN93.Rd phylosim/man/getWriteProtected.QMatrix.Rd phylosim/man/setHandler.Event.Rd phylosim/man/as.character.Event.Rd phylosim/man/MtZoa.Rd phylosim/man/sampleState.ToleranceSubstitution.Rd phylosim/man/getRateParamList.GTR.Rd phylosim/man/getProcesses.Site.Rd phylosim/man/getRateParam.F81.Rd phylosim/man/setRate.GeneralSubstitution.Rd phylosim/man/GY94.Rd phylosim/man/attachSeqToNode.PhyloSim.Rd phylosim/man/setKappa.F84.Rd phylosim/man/omegaVarM3.CodonSequence.Rd phylosim/man/getRateParamList.T92.Rd phylosim/man/is.GeneralSubstitution.Rd phylosim/man/getRateParam.GTR.Rd phylosim/man/summary.PhyloSim.Rd phylosim/man/checkConsistency.FastFieldDeletor.Rd phylosim/man/getTreeLength.PhyloSim.Rd phylosim/man/getNtips.PhyloSim.Rd phylosim/man/getCumulativeRates.Sequence.Rd phylosim/man/getProbs.DiscreteInsertor.Rd phylosim/man/setId.PhyloSim.Rd phylosim/man/plot.DiscreteInsertor.Rd phylosim/man/getWriteProtected.Alphabet.Rd phylosim/man/setGenerateBy.GeneralInsertor.Rd phylosim/man/setEquDist.ToleranceSubstitution.Rd phylosim/man/checkConsistency.Event.Rd phylosim/man/virtualAssignmentForbidden.PSRoot.Rd phylosim/man/getBaseFreqs.GTR.Rd phylosim/man/Scale.QMatrix.Rd phylosim/man/Sequence.Rd phylosim/man/setTableId.CodonAlphabet.Rd phylosim/man/setSizes.DiscreteDeletor.Rd phylosim/man/getTips.PhyloSim.Rd phylosim/man/checkConsistency.HKY.Rd phylosim/man/as.character.GeneralSubstitution.Rd phylosim/man/Event.Rd phylosim/man/AnyAlphabet.Rd phylosim/man/FastFieldDeletor.Rd phylosim/man/getEventsAtSite.Process.Rd phylosim/man/checkConsistency.F84.Rd phylosim/man/isAttached.Site.Rd phylosim/man/GeneralSubstitution.Rd phylosim/man/Alphabet.Rd phylosim/man/Debug.PhyloSim.Rd phylosim/man/PAM.dcmut.Rd phylosim/man/getRateParam.T92.Rd phylosim/man/GeneralDeletor.Rd phylosim/man/ll.PSRoot.Rd phylosim/man/getTotalRatesFromRange.Sequence.Rd phylosim/man/getParameterAtSites.Sequence.Rd phylosim/man/hasUndefinedRate.GeneralSubstitution.Rd phylosim/man/setKappa.GY94.Rd phylosim/man/ContinuousDeletor.Rd phylosim/man/plusInvGamma.Sequence.Rd phylosim/man/Site.Rd phylosim/man/is.Process.Rd phylosim/man/setMethodsList.PSRoot.Rd phylosim/man/getAlphabet.GeneralSubstitution.Rd phylosim/man/plot.PhyloSim.Rd phylosim/man/readTree.PhyloSim.Rd phylosim/man/checkConsistency.GeneralInsertor.Rd phylosim/man/plot.Sequence.Rd phylosim/man/getPhylo.PhyloSim.Rd phylosim/man/getProcess.QMatrix.Rd phylosim/man/setWriteProtected.Alphabet.Rd phylosim/man/summary.Process.Rd phylosim/man/getLengthParam2.FastFieldDeletor.Rd phylosim/man/checkConsistency.QMatrix.Rd phylosim/man/getBaseFreqs.F81.Rd phylosim/man/getString.Sequence.Rd phylosim/man/Undocumented.PhyloSim.Rd phylosim/man/setSiteSpecificParamIds.Process.Rd phylosim/man/getEventRate.GeneralSubstitution.Rd phylosim/man/summary.ContinuousInsertor.Rd phylosim/man/setId.Sequence.Rd phylosim/man/Translate.CodonSequence.Rd phylosim/man/getSites.Sequence.Rd phylosim/man/checkConsistency.DiscreteDeletor.Rd phylosim/man/as.character.Sequence.Rd phylosim/man/detachHookFromNode.PhyloSim.Rd phylosim/man/getAlignment.PhyloSim.Rd phylosim/man/getTableId.CodonAlphabet.Rd phylosim/man/F84.Rd phylosim/man/my.all.equal.PSRoot.Rd phylosim/man/checkConsistency.CodonAlphabet.Rd phylosim/man/getRateParam.HKY.Rd phylosim/man/summary.FastFieldDeletor.Rd phylosim/man/getEventsAtSite.GeneralInsertor.Rd phylosim/man/CodonSequence.Rd phylosim/man/getName.PhyloSim.Rd phylosim/man/getRateParam.K81.Rd phylosim/man/BinaryAlphabet.Rd phylosim/man/getRateList.ToleranceSubstitution.Rd phylosim/man/omegaVarM1.CodonSequence.Rd phylosim/man/getEvents.Site.Rd phylosim/man/checkConsistency.Process.Rd phylosim/man/checkConsistency.Alphabet.Rd phylosim/man/mtArt.Rd phylosim/man/summary.ToleranceSubstitution.Rd phylosim/man/setName.Event.Rd phylosim/man/is.ToleranceSubstitution.Rd phylosim/man/checkConsistency.GeneralSubstitution.Rd phylosim/man/getPosition.Event.Rd phylosim/man/WAG.Rd phylosim/man/setQMatrix.GeneralSubstitution.Rd phylosim/man/setSize.Alphabet.Rd phylosim/man/NucleotideAlphabet.Rd phylosim/man/getBaseFreqs.K81.Rd phylosim/man/setPhylo.PhyloSim.Rd phylosim/man/summary.UNREST.Rd phylosim/man/as.character.PhyloSim.Rd phylosim/man/setRateParamList.F84.Rd phylosim/man/getEventRate.QMatrix.Rd phylosim/man/stringLengthVector.Rd phylosim/man/getRateParamList.K81.Rd phylosim/man/getSizes.DiscreteInsertor.Rd phylosim/man/setRate.ToleranceSubstitution.Rd phylosim/man/getWriteProtected.Event.Rd phylosim/man/summary.CodonAlphabet.Rd phylosim/man/setTotalRate.Site.Rd phylosim/man/GeneralInsertor.Rd phylosim/man/setName.Sequence.Rd phylosim/man/rescaleQMatrix.GeneralSubstitution.Rd phylosim/man/plot.ContinuousInsertor.Rd phylosim/man/setLogFile.PhyloSim.Rd phylosim/man/summary.K80.Rd phylosim/man/readAlignment.PhyloSim.Rd phylosim/man/summary.GY94.Rd phylosim/man/setMaxLength.ContinuousInsertor.Rd phylosim/man/as.character.Site.Rd phylosim/man/getUniqueAlphabets.Sequence.Rd phylosim/man/setSizes.DiscreteInsertor.Rd phylosim/man/getAlphabet.Process.Rd phylosim/man/setEquDist.GeneralSubstitution.Rd phylosim/man/getBaseFreqs.HKY.Rd phylosim/man/setCumulativeRates.Sequence.Rd phylosim/man/is.GY94.Rd phylosim/man/T92.Rd phylosim/man/detachProcess.Site.Rd phylosim/man/setQMatrix.ToleranceSubstitution.Rd phylosim/man/setBaseFreqs.TN93.Rd phylosim/man/setSequences.PhyloSim.Rd phylosim/man/AminoAcidSequence.Rd phylosim/man/intersect.list.PSRoot.Rd phylosim/man/setSymbolLength.Alphabet.Rd phylosim/man/getSize.Alphabet.Rd phylosim/man/checkConsistency.PSRootSummary.Rd phylosim/man/setUniqueProcesses.Sequence.Rd phylosim/man/setCodonFreqs.GY94.Rd phylosim/man/getAcceptWin.GeneralInsertor.Rd phylosim/man/copySubSequence.Sequence.Rd phylosim/man/getSeqFromNode.PhyloSim.Rd phylosim/man/plot.ContinuousDeletor.Rd phylosim/man/setOmegas.CodonSequence.Rd phylosim/man/setAlphabets.Sequence.Rd phylosim/man/areSynonymous.CodonAlphabet.Rd phylosim/man/TN93.Rd phylosim/man/setEvents.Site.Rd phylosim/man/is.Site.Rd phylosim/man/getLengthParam1.FastFieldDeletor.Rd phylosim/man/setComments.PSRoot.Rd phylosim/man/clone.Sequence.Rd phylosim/man/summary.TN93.Rd phylosim/man/getRateParamList.F84.Rd phylosim/man/getProbs.DiscreteDeletor.Rd phylosim/man/checkConsistency.PhyloSim.Rd phylosim/man/setString.Sequence.Rd phylosim/man/summary.K81.Rd phylosim/man/generateInsert.GeneralInsertor.Rd phylosim/man/getRateParamList.K80.Rd phylosim/man/getId.QMatrix.Rd phylosim/man/getSequence.Site.Rd phylosim/man/summary.GeneralInDel.Rd phylosim/man/NucleotideSequence.Rd phylosim/man/setMatrix.QMatrix.Rd phylosim/man/setTotalRates.Sequence.Rd phylosim/man/checkConsistency.PSRoot.Rd phylosim/man/omegaVarM4.CodonSequence.Rd phylosim/man/checkConsistency.TN93.Rd phylosim/man/getName.QMatrix.Rd phylosim/man/getNedges.PhyloSim.Rd phylosim/man/getAncestral.Site.Rd phylosim/man/setRateParamList.F81.Rd phylosim/man/setParameterAtSites.Sequence.Rd phylosim/man/getSiteSpecificParamList.Process.Rd phylosim/man/setRate.Event.Rd phylosim/man/setStates.Sequence.Rd phylosim/man/getRateParam.TN93.Rd phylosim/man/getSite.Event.Rd phylosim/man/000==.Process.Rd phylosim/man/plot.GeneralSubstitution.Rd phylosim/man/Simulate.PhyloSim.Rd phylosim/man/getMethodsList.PSRoot.Rd phylosim/man/summary.GeneralDeletor.Rd phylosim/man/setLogLevel.PhyloSim.Rd phylosim/man/clone.ToleranceSubstitution.Rd phylosim/man/getRateParamList.F81.Rd phylosim/man/isEmpty.Alphabet.Rd phylosim/man/getId.PhyloSim.Rd phylosim/man/setName.PhyloSim.Rd phylosim/man/setLengthParam1.FastFieldDeletor.Rd phylosim/man/getRate.ToleranceSubstitution.Rd phylosim/man/setTipLabels.PhyloSim.Rd phylosim/man/setAncestral.Sequence.Rd phylosim/man/globalConsistencyCheck.PSRoot.Rd phylosim/man/getRootNode.PhyloSim.Rd phylosim/man/ToleranceSubstitution.Rd phylosim/man/setProbs.DiscreteDeletor.Rd phylosim/man/setWriteProtected.Event.Rd phylosim/man/setRateParam.GTR.Rd phylosim/man/PSRoot.Rd phylosim/man/setBigRate.Sequence.Rd phylosim/man/summary.Site.Rd phylosim/man/AminoAcidAlphabet.Rd phylosim/man/JTT.Rd phylosim/man/checkConsistency.JC69.Rd phylosim/man/isStartCodon.CodonAlphabet.Rd phylosim/man/setTheta.T92.Rd phylosim/man/checkConsistency.CodonUNREST.Rd phylosim/man/is.Alphabet.Rd phylosim/man/getRootSeq.PhyloSim.Rd phylosim/man/ECMrest.Rd phylosim/man/getTotalRates.Sequence.Rd phylosim/man/getRateParam.K80.Rd phylosim/man/sampleStates.Sequence.Rd phylosim/man/CodonUNREST.Rd phylosim/man/getTheta.T92.Rd phylosim/man/getEventsAtSite.GeneralSubstitution.Rd phylosim/man/getNodes.PhyloSim.Rd phylosim/man/checkConsistency.CodonSubst.Rd phylosim/man/getDist.ContinuousInsertor.Rd phylosim/man/plot.DiscreteDeletor.Rd phylosim/man/getId.Process.Rd phylosim/man/is.phylo.Rd phylosim/man/setId.Process.Rd phylosim/man/setRateParamList.TN93.Rd phylosim/man/is.PSRoot.Rd phylosim/man/getProcess.Event.Rd phylosim/man/setState.Site.Rd phylosim/man/K81.Rd phylosim/man/setInsertHook.GeneralInsertor.Rd phylosim/man/setProcess.Event.Rd phylosim/man/setBaseFreqs.F81.Rd phylosim/man/is.Sequence.Rd phylosim/man/getLength.Sequence.Rd phylosim/man/getInsertionTolerance.Sequence.Rd phylosim/man/getLogLevel.PhyloSim.Rd phylosim/man/newMatrix.CodonSubst.Rd phylosim/man/setRateParamList.T92.Rd phylosim/man/F81.Rd phylosim/man/sampleState.GeneralSubstitution.Rd phylosim/man/setId.QMatrix.Rd phylosim/man/getSequences.PhyloSim.Rd phylosim/man/000==.Alphabet.Rd phylosim/man/setRateParam.TN93.Rd phylosim/man/scaleTree.PhyloSim.Rd phylosim/man/getSizes.DiscreteDeletor.Rd phylosim/man/plot.ToleranceSubstitution.Rd phylosim/man/setRateParamList.HKY.Rd phylosim/man/getId.Sequence.Rd phylosim/man/exportStatTree.PhyloSim.Rd phylosim/man/DiscreteInsertor.Rd phylosim/man/AminoAcidSubst.Rd phylosim/man/summary.AminoAcidSubst.Rd phylosim/man/summary.JC69.Rd phylosim/man/omegaHist.CodonSequence.Rd phylosim/man/setDist.ContinuousInsertor.Rd phylosim/man/getMaxLength.ContinuousDeletor.Rd phylosim/man/setSite.Event.Rd phylosim/man/setProcesses.Site.Rd phylosim/man/getRate.QMatrix.Rd phylosim/man/setSymbols.Alphabet.Rd phylosim/man/getEventsAtSite.GY94.Rd phylosim/man/setScale.BrownianInsertor.Rd phylosim/man/GTR.Rd phylosim/man/getSymbols.Alphabet.Rd phylosim/man/getCodonFreqs.GY94.Rd phylosim/man/is.na.PSRoot.Rd phylosim/man/summary.QMatrix.Rd phylosim/man/setWriteProtected.Sequence.Rd phylosim/man/setInsertionTolerance.Sequence.Rd phylosim/man/getRate.GeneralSubstitution.Rd phylosim/man/setNedges.PhyloSim.Rd phylosim/man/PAM.Rd phylosim/man/getEventRate.ToleranceSubstitution.Rd phylosim/man/summary.T92.Rd phylosim/man/translateCodon.CodonAlphabet.Rd phylosim/man/setUniqueAlphabets.Sequence.Rd phylosim/man/getRateParam.F84.Rd phylosim/man/getScaledMatrix.QMatrix.Rd phylosim/man/setBaseFreqs.HKY.Rd phylosim/man/attachProcess.Sequence.Rd phylosim/man/checkConsistency.Site.Rd phylosim/man/getAlphabet.ToleranceSubstitution.Rd phylosim/man/getQMatrix.GeneralSubstitution.Rd phylosim/man/getType.Alphabet.Rd phylosim/man/revComp.NucleotideSequence.Rd phylosim/man/setSequence.Site.Rd phylosim/man/GeneralInDel.Rd phylosim/man/getTotalRate.Site.Rd phylosim/man/getAlphabets.Sequence.Rd phylosim/man/getRateMultipliers.Sequence.Rd phylosim/man/getEventsAtSite.FastFieldDeletor.Rd phylosim/man/saveAlignment.PhyloSim.Rd phylosim/man/getBaseFreqs.K80.Rd phylosim/man/LG.Rd phylosim/man/is.QMatrix.Rd phylosim/man/setProcesses.Sequence.Rd phylosim/man/mtREV24.Rd phylosim/man/JTT.dcmut.Rd phylosim/man/checkConsistency.UNREST.Rd phylosim/man/getQMatrix.ToleranceSubstitution.Rd phylosim/man/summary.BinarySubst.Rd phylosim/man/isStopCodon.CodonAlphabet.Rd phylosim/man/setTreeLength.PhyloSim.Rd phylosim/man/getBigRate.Sequence.Rd phylosim/man/getBaseFreqs.F84.Rd phylosim/man/is.CodonAlphabet.Rd phylosim/man/setAcceptWin.GeneralInsertor.Rd phylosim/man/checkConsistency.F81.Rd phylosim/man/getState.Site.Rd phylosim/man/summary.Alphabet.Rd phylosim/man/setProcess.QMatrix.Rd phylosim/man/setRateParam.K80.Rd phylosim/man/DiscreteDeletor.Rd phylosim/man/setToleranceMargin.FastFieldDeletor.Rd phylosim/man/plusGamma.Sequence.Rd phylosim/man/getAlignmentLength.PhyloSim.Rd phylosim/man/setRootNode.PhyloSim.Rd phylosim/man/K80.Rd phylosim/man/setSiteSpecificParamList.Process.Rd phylosim/man/CodonSubst.Rd phylosim/man/summary.Event.Rd phylosim/man/getUniqueProcesses.Sequence.Rd phylosim/man/getStates.Sequence.Rd phylosim/man/setBaseFreqs.K80.Rd phylosim/man/mtMam.Rd phylosim/man/BinarySequence.Rd phylosim/man/clearStates.Sequence.Rd phylosim/man/getWriteProtected.Process.Rd phylosim/man/detachProcess.Sequence.Rd phylosim/man/setNodes.PhyloSim.Rd phylosim/man/Process.Rd
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