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

Functions

all Man page
Alphabet Man page
==.Alphabet Man page
!=.Alphabet Man page
Alphabet.== Man page
Alphabet.as.character Man page
Alphabet.checkConsistency Man page
Alphabet.getSize Man page
Alphabet.getSymbolLength Man page
Alphabet.getSymbols Man page
Alphabet.getType Man page
Alphabet.getWriteProtected Man page
Alphabet.hasSymbols Man page
Alphabet.isEmpty Man page
==,Alphabet-method Man page
Alphabet.setSize Man page
Alphabet.setSymbolLength Man page
Alphabet.setSymbols Man page
Alphabet.setType Man page
Alphabet.setWriteProtected Man page
Alphabet.summary Man page
AminoAcidAlphabet Man page
AminoAcidSequence Man page
AminoAcidSubst Man page
AminoAcidSubst.buildFromPAML Man page
AminoAcidSubst.checkConsistency Man page
AminoAcidSubst.newAAMatrix Man page
AminoAcidSubst.summary Man page
AnyAlphabet Man page
areSynonymous Man page
areSynonymous.CodonAlphabet Man page
areSynonymous,CodonAlphabet-method Man page
as.character.Alphabet Man page
as.character,Alphabet-method Man page
as.character.Event Man page
as.character,Event-method Man page
as.character.GeneralSubstitution Man page
as.character,GeneralSubstitution-method Man page
as.character.PhyloSim Man page
as.character,PhyloSim-method Man page
as.character.Process Man page
as.character,Process-method Man page
as.character.QMatrix Man page
as.character,QMatrix-method Man page
as.character.Sequence Man page
as.character,Sequence-method Man page
as.character.Site Man page
as.character,Site-method Man page
as.character.ToleranceSubstitution Man page
as.character,ToleranceSubstitution-method Man page
attachHookToNode Man page
attachHookToNode.PhyloSim Man page
attachHookToNode,PhyloSim-method Man page
attachProcess Man page
attachProcess.Sequence Man page
attachProcess,Sequence-method Man page
attachProcess.Site Man page
attachProcess,Site-method Man page
attachSeqToNode Man page
attachSeqToNode.PhyloSim Man page
attachSeqToNode,PhyloSim-method Man page
BinaryAlphabet Man page
BinarySequence Man page
BinarySubst Man page
BinarySubst.checkConsistency Man page
BinarySubst.summary Man page
BrownianInsertor Man page
BrownianInsertor.BrownianPath Man page
BrownianInsertor.checkConsistency Man page
BrownianInsertor.getScale Man page
BrownianInsertor.getType Man page
BrownianInsertor.setScale Man page
BrownianInsertor.setType Man page
BrownianInsertor.summary Man page
BrownianPath Man page
BrownianPath.BrownianInsertor Man page
BrownianPath,BrownianInsertor-method Man page
buildFromPAML Man page
buildFromPAML.AminoAcidSubst Man page
buildFromPAML,AminoAcidSubst-method Man page
buildFromPAML.CodonSubst Man page
buildFromPAML,CodonSubst-method Man page
checkConsistency Man page
checkConsistency.Alphabet Man page
checkConsistency,Alphabet-method Man page
checkConsistency.AminoAcidSubst Man page
checkConsistency,AminoAcidSubst-method Man page
checkConsistency.BinarySubst Man page
checkConsistency,BinarySubst-method Man page
checkConsistency.BrownianInsertor Man page
checkConsistency,BrownianInsertor-method Man page
checkConsistency.CodonAlphabet Man page
checkConsistency,CodonAlphabet-method Man page
checkConsistency.CodonSequence Man page
checkConsistency,CodonSequence-method Man page
checkConsistency.CodonSubst Man page
checkConsistency,CodonSubst-method Man page
checkConsistency.CodonUNREST Man page
checkConsistency,CodonUNREST-method Man page
checkConsistency.ContinuousDeletor Man page
checkConsistency,ContinuousDeletor-method Man page
checkConsistency.ContinuousInsertor Man page
checkConsistency,ContinuousInsertor-method Man page
checkConsistency.DiscreteDeletor Man page
checkConsistency,DiscreteDeletor-method Man page
checkConsistency.DiscreteInsertor Man page
checkConsistency,DiscreteInsertor-method Man page
checkConsistency.Event Man page
checkConsistency,Event-method Man page
checkConsistency.F81 Man page
checkConsistency,F81-method Man page
checkConsistency.F84 Man page
checkConsistency,F84-method Man page
checkConsistency.FastFieldDeletor Man page
checkConsistency,FastFieldDeletor-method Man page
checkConsistency.GeneralDeletor Man page
checkConsistency,GeneralDeletor-method Man page
checkConsistency.GeneralInDel Man page
checkConsistency,GeneralInDel-method Man page
checkConsistency.GeneralInsertor Man page
checkConsistency,GeneralInsertor-method Man page
checkConsistency.GeneralSubstitution Man page
checkConsistency,GeneralSubstitution-method Man page
checkConsistency.GTR Man page
checkConsistency,GTR-method Man page
checkConsistency.GY94 Man page
checkConsistency,GY94-method Man page
checkConsistency.HKY Man page
checkConsistency,HKY-method Man page
checkConsistency.JC69 Man page
checkConsistency,JC69-method Man page
checkConsistency.K80 Man page
checkConsistency,K80-method Man page
checkConsistency.K81 Man page
checkConsistency,K81-method Man page
checkConsistency.PhyloSim Man page
checkConsistency,PhyloSim-method Man page
checkConsistency.Process Man page
checkConsistency,Process-method Man page
checkConsistency.PSRoot Man page
checkConsistency,PSRoot-method Man page
checkConsistency.PSRootSummary Man page
checkConsistency,PSRootSummary-method Man page
checkConsistency.QMatrix Man page
checkConsistency,QMatrix-method Man page
checkConsistency.Sequence Man page
checkConsistency,Sequence-method Man page
checkConsistency.Site Man page
checkConsistency,Site-method Man page
checkConsistency.T92 Man page
checkConsistency,T92-method Man page
checkConsistency.TN93 Man page
checkConsistency,TN93-method Man page
checkConsistency.ToleranceSubstitution Man page
checkConsistency,ToleranceSubstitution-method Man page
checkConsistency.UNREST Man page
checkConsistency,UNREST-method Man page
clearStates Man page
clearStates.Sequence Man page
clearStates,Sequence-method Man page
clone.GeneralSubstitution Man page
clone,GeneralSubstitution-method Man page
clone.Process Man page
clone,Process-method Man page
clone.Sequence Man page
clone,Sequence-method Man page
clone.ToleranceSubstitution Man page
clone,ToleranceSubstitution-method Man page
CodonAlphabet Man page
CodonAlphabet.areSynonymous Man page
CodonAlphabet.checkConsistency Man page
CodonAlphabet.getTableId Man page
CodonAlphabet.getTransTable Man page
CodonAlphabet.isStartCodon Man page
CodonAlphabet.isStopCodon Man page
CodonAlphabet.setTableId Man page
CodonAlphabet.setTransTable Man page
CodonAlphabet.summary Man page
CodonAlphabet.translateCodon Man page
CodonSequence Man page
CodonSequence.checkConsistency Man page
CodonSequence.getOmegas Man page
CodonSequence.omegaHist Man page
CodonSequence.omegaVarM0 Man page
CodonSequence.omegaVarM1 Man page
CodonSequence.omegaVarM2 Man page
CodonSequence.omegaVarM3 Man page
CodonSequence.omegaVarM4 Man page
CodonSequence.setOmegas Man page
CodonSequence.Translate Man page
CodonSubst Man page
CodonSubst.buildFromPAML Man page
CodonSubst.checkConsistency Man page
CodonSubst.newMatrix Man page
CodonSubst.summary Man page
CodonUNREST Man page
CodonUNREST.checkConsistency Man page
ContinuousDeletor Man page
ContinuousDeletor.checkConsistency Man page
ContinuousDeletor.getDist Man page
ContinuousDeletor.getMaxLength Man page
ContinuousDeletor.plot Man page
ContinuousDeletor.setDist Man page
ContinuousDeletor.setMaxLength Man page
ContinuousDeletor.summary Man page
ContinuousInsertor Man page
ContinuousInsertor.checkConsistency Man page
ContinuousInsertor.getDist Man page
ContinuousInsertor.getMaxLength Man page
ContinuousInsertor.plot Man page
ContinuousInsertor.setDist Man page
ContinuousInsertor.setMaxLength Man page
ContinuousInsertor.summary Man page
copySubSequence Man page
copySubSequence.Sequence Man page
copySubSequence,Sequence-method Man page
cpREV Man page
Debug Man page
Debug.PhyloSim Man page
Debug,PhyloSim-method Man page
default Man page
deleteSubSequence Man page
deleteSubSequence.Sequence Man page
deleteSubSequence,Sequence-method Man page
detachHookFromNode Man page
detachHookFromNode.PhyloSim Man page
detachHookFromNode,PhyloSim-method Man page
detachProcess Man page
detachProcess.Sequence Man page
detachProcess,Sequence-method Man page
detachProcess.Site Man page
detachProcess,Site-method Man page
detachSeqFromNode Man page
detachSeqFromNode.PhyloSim Man page
detachSeqFromNode,PhyloSim-method Man page
DiscreteDeletor Man page
DiscreteDeletor.checkConsistency Man page
DiscreteDeletor.getProbs Man page
DiscreteDeletor.getSizes Man page
DiscreteDeletor.plot Man page
DiscreteDeletor.setProbs Man page
DiscreteDeletor.setSizes Man page
DiscreteDeletor.summary Man page
DiscreteInsertor Man page
DiscreteInsertor.checkConsistency Man page
DiscreteInsertor.getProbs Man page
DiscreteInsertor.getSizes Man page
DiscreteInsertor.plot Man page
DiscreteInsertor.setProbs Man page
DiscreteInsertor.setSizes Man page
DiscreteInsertor.summary Man page
ECMrest Man page
ECMunrest Man page
enableVirtual Man page
enableVirtual.PSRoot Man page
enableVirtual,PSRoot-method Man page
equal Man page
Event Man page
Event.as.character Man page
Event.checkConsistency Man page
Event.getHandler Man page
Event.getName Man page
Event.getPosition Man page
Event.getProcess Man page
Event.getRate Man page
Event.getSite Man page
Event.getWriteProtected Man page
Event.Perform Man page
Event.setHandler Man page
Event.setName Man page
Event.setPosition Man page
Event.setProcess Man page
Event.setRate Man page
Event.setSite Man page
Event.setWriteProtected Man page
Event.summary Man page
exportStatTree Man page
exportStatTree.PhyloSim Man page
exportStatTree,PhyloSim-method Man page
F81 Man page
F81.checkConsistency Man page
F81.getBaseFreqs Man page
F81.getRateParam Man page
F81.getRateParamList Man page
F81.setBaseFreqs Man page
F81.setRateParam Man page
F81.setRateParamList Man page
F81.summary Man page
F84 Man page
F84.checkConsistency Man page
F84.getBaseFreqs Man page
F84.getKappa Man page
F84.getRateParam Man page
F84.getRateParamList Man page
F84.setBaseFreqs Man page
F84.setKappa Man page
F84.setRateParam Man page
F84.setRateParamList Man page
F84.summary Man page
FastFieldDeletor Man page
FastFieldDeletor.checkConsistency Man page
FastFieldDeletor.getEventsAtSite Man page
FastFieldDeletor.getLengthParam1 Man page
FastFieldDeletor.getLengthParam2 Man page
FastFieldDeletor.getToleranceMargin Man page
FastFieldDeletor.getType Man page
FastFieldDeletor.setLengthParam1 Man page
FastFieldDeletor.setLengthParam2 Man page
FastFieldDeletor.setToleranceMargin Man page
FastFieldDeletor.setType Man page
FastFieldDeletor.summary Man page
flagTotalRate Man page
flagTotalRate.Site Man page
flagTotalRate,Site-method Man page
GeneralDeletor Man page
GeneralDeletor.checkConsistency Man page
GeneralDeletor.getEventsAtSite Man page
GeneralDeletor.summary Man page
GeneralInDel Man page
GeneralInDel.checkConsistency Man page
GeneralInDel.getAcceptBy Man page
GeneralInDel.getProposeBy Man page
GeneralInDel.getRate Man page
GeneralInDel.hasUndefinedRate Man page
GeneralInDel.proposeLength Man page
GeneralInDel.setAcceptBy Man page
GeneralInDel.setProposeBy Man page
GeneralInDel.setRate Man page
GeneralInDel.summary Man page
GeneralInsertor Man page
GeneralInsertor.checkConsistency Man page
GeneralInsertor.generateInsert Man page
GeneralInsertor.getAcceptWin Man page
GeneralInsertor.getEventsAtSite Man page
GeneralInsertor.getGenerateBy Man page
GeneralInsertor.getInsertHook Man page
GeneralInsertor.getTemplateSeq Man page
GeneralInsertor.setAcceptWin Man page
GeneralInsertor.setGenerateBy Man page
GeneralInsertor.setInsertHook Man page
GeneralInsertor.setTemplateSeq Man page
GeneralInsertor.summary Man page
GeneralSubstitution Man page
GeneralSubstitution.as.character Man page
GeneralSubstitution.checkConsistency Man page
GeneralSubstitution.clone Man page
GeneralSubstitution.getAlphabet Man page
GeneralSubstitution.getEquDist Man page
GeneralSubstitution.getEventRate Man page
GeneralSubstitution.getEventRateAtSite Man page
GeneralSubstitution.getEventsAtSite Man page
GeneralSubstitution.getQMatrix Man page
GeneralSubstitution.getRate Man page
GeneralSubstitution.getRateList Man page
GeneralSubstitution.hasUndefinedRate Man page
GeneralSubstitution.plot Man page
GeneralSubstitution.rescaleQMatrix Man page
GeneralSubstitution.sampleState Man page
GeneralSubstitution.setAlphabet Man page
GeneralSubstitution.setEquDist Man page
GeneralSubstitution.setQMatrix Man page
GeneralSubstitution.setRate Man page
GeneralSubstitution.setRateList Man page
GeneralSubstitution.summary Man page
generateInsert Man page
generateInsert.GeneralInsertor Man page
generateInsert,GeneralInsertor-method Man page
getAcceptBy Man page
getAcceptBy.GeneralInDel Man page
getAcceptBy,GeneralInDel-method Man page
getAcceptBy.GeneralInsertor Man page
getAcceptWin Man page
getAcceptWin.GeneralInsertor Man page
getAcceptWin,GeneralInsertor-method Man page
getAlignment Man page
getAlignmentLength Man page
getAlignmentLength.PhyloSim Man page
getAlignmentLength,PhyloSim-method Man page
getAlignment.PhyloSim Man page
getAlignment,PhyloSim-method Man page
getAlphabet Man page
getAlphabet Man page
getAlphabet.GeneralSubstitution Man page
getAlphabet,GeneralSubstitution-method Man page
getAlphabet.Process Man page
getAlphabet,Process-method Man page
getAlphabet.QMatrix Man page
getAlphabet,QMatrix-method Man page
getAlphabets Man page
getAlphabet.Site Man page
getAlphabet,Site-method Man page
getAlphabets.Sequence Man page
getAlphabets,Sequence-method Man page
getAlphabet.ToleranceSubstitution Man page
getAlphabet,ToleranceSubstitution-method Man page
getAncestral Man page
getAncestral Man page
getAncestral.Sequence Man page
getAncestral,Sequence-method Man page
getAncestral.Site Man page
getAncestral,Site-method Man page
getBaseFreqs Man page
getBaseFreqs.F81 Man page
getBaseFreqs,F81-method Man page
getBaseFreqs.F84 Man page
getBaseFreqs,F84-method Man page
getBaseFreqs.GTR Man page
getBaseFreqs,GTR-method Man page
getBaseFreqs.HKY Man page
getBaseFreqs,HKY-method Man page
getBaseFreqs.K80 Man page
getBaseFreqs,K80-method Man page
getBaseFreqs.K81 Man page
getBaseFreqs,K81-method Man page
getBaseFreqs.TN93 Man page
getBaseFreqs,TN93-method Man page
getBigRate Man page
getBigRate.Sequence Man page
getBigRate,Sequence-method Man page
getBranchEvents Man page
getBranchEvents.PhyloSim Man page
getBranchEvents,PhyloSim-method Man page
getCodonFreqs Man page
getCodonFreqs.GY94 Man page
getCodonFreqs,GY94-method Man page
getComments Man page
getComments.PSRoot Man page
getComments,PSRoot-method Man page
getCumulativeRates Man page
getCumulativeRatesFromRange Man page
getCumulativeRatesFromRange.Sequence Man page
getCumulativeRatesFromRange,Sequence-method Man page
getCumulativeRates.Sequence Man page
getCumulativeRates,Sequence-method Man page
getDeletionTolerance Man page
getDeletionTolerance.Sequence Man page
getDeletionTolerance,Sequence-method Man page
getDist Man page
getDist.ContinuousDeletor Man page
getDist,ContinuousDeletor-method Man page
getDist.ContinuousInsertor Man page
getDist,ContinuousInsertor-method Man page
getEdge Man page
getEdge.PhyloSim Man page
getEdge,PhyloSim-method Man page
getEdges Man page
getEdges.PhyloSim Man page
getEdges,PhyloSim-method Man page
getEquDist Man page
getEquDist.GeneralSubstitution Man page
getEquDist,GeneralSubstitution-method Man page
getEquDist.ToleranceSubstitution Man page
getEquDist,ToleranceSubstitution-method Man page
getEventRate Man page
getEventRateAtSite Man page
getEventRateAtSite.GeneralSubstitution Man page
getEventRateAtSite,GeneralSubstitution-method Man page
getEventRateAtSite.ToleranceSubstitution Man page
getEventRateAtSite,ToleranceSubstitution-method Man page
getEventRate.GeneralSubstitution Man page
getEventRate,GeneralSubstitution-method Man page
getEventRate.QMatrix Man page
getEventRate,QMatrix-method Man page
getEventRate.ToleranceSubstitution Man page
getEventRate,ToleranceSubstitution-method Man page
getEvents Man page
getEventsAtSite Man page
getEventsAtSite.FastFieldDeletor Man page
getEventsAtSite,FastFieldDeletor-method Man page
getEventsAtSite.GeneralDeletor Man page
getEventsAtSite,GeneralDeletor-method Man page
getEventsAtSite.GeneralInsertor Man page
getEventsAtSite,GeneralInsertor-method Man page
getEventsAtSite.GeneralSubstitution Man page
getEventsAtSite,GeneralSubstitution-method Man page
getEventsAtSite.GY94 Man page
getEventsAtSite,GY94-method Man page
getEventsAtSite.Process Man page
getEventsAtSite,Process-method Man page
getEventsAtSite.ToleranceSubstitution Man page
getEventsAtSite,ToleranceSubstitution-method Man page
getEvents.Sequence Man page
getEvents,Sequence-method Man page
getEvents.Site Man page
getEvents,Site-method Man page
getGenerateBy Man page
getGenerateBy.GeneralInsertor Man page
getGenerateBy,GeneralInsertor-method Man page
getHandler Man page
getHandler.Event Man page
getHandler,Event-method Man page
getId Man page
getId.PhyloSim Man page
getId,PhyloSim-method Man page
getId.Process Man page
getId,Process-method Man page
getId.QMatrix Man page
getId,QMatrix-method Man page
getId.Sequence Man page
getId,Sequence-method Man page
getInsertHook Man page
getInsertHook.GeneralInsertor Man page
getInsertHook,GeneralInsertor-method Man page
getInsertionTolerance Man page
getInsertionTolerance Man page
getInsertionTolerance.Sequence Man page
getInsertionTolerance,Sequence-method Man page
getKappa Man page
getKappa.F84 Man page
getKappa,F84-method Man page
getKappa.GY94 Man page
getKappa,GY94-method Man page
getLength Man page
getLengthParam1 Man page
getLengthParam1.FastFieldDeletor Man page
getLengthParam1,FastFieldDeletor-method Man page
getLengthParam2 Man page
getLengthParam2.FastFieldDeletor Man page
getLengthParam2,FastFieldDeletor-method Man page
getLength.Sequence Man page
getLength,Sequence-method Man page
getLogFile Man page
getLogFile.PhyloSim Man page
getLogFile,PhyloSim-method Man page
getLogLevel Man page
getLogLevel.PhyloSim Man page
getLogLevel,PhyloSim-method Man page
getMatrix Man page
getMatrix.QMatrix Man page
getMatrix,QMatrix-method Man page
getMaxLength Man page
getMaxLength.ContinuousDeletor Man page
getMaxLength,ContinuousDeletor-method Man page
getMaxLength.ContinuousInsertor Man page
getMaxLength,ContinuousInsertor-method Man page
getMethodsList Man page
getMethodsList.PSRoot Man page
getMethodsList,PSRoot-method Man page
getName.Event Man page
getName,Event-method Man page
getName.PhyloSim Man page
getName,PhyloSim-method Man page
getName.Process Man page
getName,Process-method Man page
getName.QMatrix Man page
getName,QMatrix-method Man page
getName.Sequence Man page
getName,Sequence-method Man page
getNedges Man page
getNedges.PhyloSim Man page
getNedges,PhyloSim-method Man page
getNodes Man page
getNodes.PhyloSim Man page
getNodes,PhyloSim-method Man page
getNtips Man page
getNtips.PhyloSim Man page
getNtips,PhyloSim-method Man page
getOmegas Man page
getOmegaScalingFactor Man page
getOmegaScalingFactor.GY94 Man page
getOmegaScalingFactor,GY94-method Man page
getOmegas.CodonSequence Man page
getOmegas,CodonSequence-method Man page
getOmegas.Sequence Man page
getParameterAtSite Man page
getParameterAtSite.Process Man page
getParameterAtSite,Process-method Man page
getParameterAtSites Man page
getParameterAtSites.Sequence Man page
getParameterAtSites,Sequence-method Man page
getPhylo Man page
getPhylo.PhyloSim Man page
getPhylo,PhyloSim-method Man page
getPosition.Event Man page
getPosition,Event-method Man page
getProbs Man page
getProbs.DiscreteDeletor Man page
getProbs,DiscreteDeletor-method Man page
getProbs.DiscreteInsertor Man page
getProbs,DiscreteInsertor-method Man page
getProcess Man page
getProcesses Man page
getProcesses.Sequence Man page
getProcesses,Sequence-method Man page
getProcesses.Site Man page
getProcesses,Site-method Man page
getProcess.Event Man page
getProcess,Event-method Man page
getProcess.QMatrix Man page
getProcess,QMatrix-method Man page
getProposeBy Man page
getProposeBy.GeneralInDel Man page
getProposeBy,GeneralInDel-method Man page
getProposeBy.GeneralInsertor Man page
getQMatrix Man page
getQMatrix.GeneralSubstitution Man page
getQMatrix,GeneralSubstitution-method Man page
getQMatrix.ToleranceSubstitution Man page
getQMatrix,ToleranceSubstitution-method Man page
getRate Man page
getRate.Event Man page
getRate,Event-method Man page
getRate.GeneralInDel Man page
getRate,GeneralInDel-method Man page
getRate.GeneralSubstitution Man page
getRate,GeneralSubstitution-method Man page
getRateList Man page
getRateList.GeneralSubstitution Man page
getRateList,GeneralSubstitution-method Man page
getRateList.QMatrix Man page
getRateList,QMatrix-method Man page
getRateList.ToleranceSubstitution Man page
getRateList,ToleranceSubstitution-method Man page
getRateMultipliers Man page
getRateMultipliers.Sequence Man page
getRateMultipliers,Sequence-method Man page
getRateParam Man page
getRateParam.F81 Man page
getRateParam,F81-method Man page
getRateParam.F84 Man page
getRateParam,F84-method Man page
getRateParam.GTR Man page
getRateParam,GTR-method Man page
getRateParam.HKY Man page
getRateParam,HKY-method Man page
getRateParam.K80 Man page
getRateParam,K80-method Man page
getRateParam.K81 Man page
getRateParam,K81-method Man page
getRateParamList Man page
getRateParamList.F81 Man page
getRateParamList,F81-method Man page
getRateParamList.F84 Man page
getRateParamList,F84-method Man page
getRateParamList.GTR Man page
getRateParamList,GTR-method Man page
getRateParamList.HKY Man page
getRateParamList,HKY-method Man page
getRateParamList.K80 Man page
getRateParamList,K80-method Man page
getRateParamList.K81 Man page
getRateParamList,K81-method Man page
getRateParamList.T92 Man page
getRateParamList,T92-method Man page
getRateParamList.TN93 Man page
getRateParamList,TN93-method Man page
getRateParam.T92 Man page
getRateParam,T92-method Man page
getRateParam.TN93 Man page
getRateParam,TN93-method Man page
getRate.QMatrix Man page
getRate,QMatrix-method Man page
getRate.ToleranceSubstitution Man page
getRate,ToleranceSubstitution-method Man page
getRootNode Man page
getRootNode.PhyloSim Man page
getRootNode,PhyloSim-method Man page
getRootSeq Man page
getRootSeq.PhyloSim Man page
getRootSeq,PhyloSim-method Man page
getScale Man page
getScale.BrownianInsertor Man page
getScale,BrownianInsertor-method Man page
getScaledMatrix Man page
getScaledMatrix.QMatrix Man page
getScaledMatrix,QMatrix-method Man page
getSeqFromNode Man page
getSeqFromNode.PhyloSim Man page
getSeqFromNode,PhyloSim-method Man page
getSequence Man page
getSequences Man page
getSequence.Site Man page
getSequence,Site-method Man page
getSequences.PhyloSim Man page
getSequences,PhyloSim-method Man page
getSite Man page
getSite.Event Man page
getSite,Event-method Man page
getSites Man page
getSiteSpecificParamIds Man page
getSiteSpecificParamIds.Process Man page
getSiteSpecificParamIds,Process-method Man page
getSiteSpecificParamList Man page
getSiteSpecificParamList.Process Man page
getSiteSpecificParamList,Process-method Man page
getSites.Sequence Man page
getSites,Sequence-method Man page
getSize Man page
getSize.Alphabet Man page
getSize,Alphabet-method Man page
getSizes Man page
getSizes.DiscreteDeletor Man page
getSizes,DiscreteDeletor-method Man page
getSizes.DiscreteInsertor Man page
getSizes,DiscreteInsertor-method Man page
getState Man page
getStates Man page
getState.Site Man page
getState,Site-method Man page
getStates.Sequence Man page
getStates,Sequence-method Man page
getString Man page
getString.Sequence Man page
getString,Sequence-method Man page
getSymbolFreqs Man page
getSymbolFreqs.Sequence Man page
getSymbolFreqs,Sequence-method Man page
getSymbolLength Man page
getSymbolLength.Alphabet Man page
getSymbolLength,Alphabet-method Man page
getSymbols Man page
getSymbols.Alphabet Man page
getSymbols,Alphabet-method Man page
getTableId Man page
getTableId.CodonAlphabet Man page
getTableId,CodonAlphabet-method Man page
getTargetState Man page
getTemplateSeq Man page
getTemplateSeq.GeneralInsertor Man page
getTemplateSeq,GeneralInsertor-method Man page
getTheta Man page
getTheta.T92 Man page
getTheta,T92-method Man page
getTipLabels Man page
getTipLabels.PhyloSim Man page
getTipLabels,PhyloSim-method Man page
getTips Man page
getTips.PhyloSim Man page
getTips,PhyloSim-method Man page
getToleranceMargin Man page
getToleranceMargin.FastFieldDeletor Man page
getToleranceMargin,FastFieldDeletor-method Man page
getTotalRate Man page
getTotalRates Man page
getTotalRatesFromRange Man page
getTotalRatesFromRange.Sequence Man page
getTotalRatesFromRange,Sequence-method Man page
getTotalRate.Site Man page
getTotalRate,Site-method Man page
getTotalRates.Sequence Man page
getTotalRates,Sequence-method Man page
getTransTable Man page
getTransTable.CodonAlphabet Man page
getTransTable,CodonAlphabet-method Man page
getTreeLength Man page
getTreeLength.PhyloSim Man page
getTreeLength,PhyloSim-method Man page
getType Man page
getType.Alphabet Man page
getType,Alphabet-method Man page
getType.BrownianInsertor Man page
getType,BrownianInsertor-method Man page
getType.FastFieldDeletor Man page
getType,FastFieldDeletor-method Man page
getUniqueAlphabets Man page
getUniqueAlphabets.Sequence Man page
getUniqueAlphabets,Sequence-method Man page
getUniqueProcesses Man page
getUniqueProcesses.Sequence Man page
getUniqueProcesses,Sequence-method Man page
getWriteProtected Man page
getWriteProtected.Alphabet Man page
getWriteProtected,Alphabet-method Man page
getWriteProtected.Event Man page
getWriteProtected,Event-method Man page
getWriteProtected.Process Man page
getWriteProtected,Process-method Man page
getWriteProtected.QMatrix Man page
getWriteProtected,QMatrix-method Man page
getWriteProtected.Sequence Man page
getWriteProtected,Sequence-method Man page
globalConsistencyCheck Man page
globalConsistencyCheck.PSRoot Man page
globalConsistencyCheck,PSRoot-method Man page
GTR Man page
GTR.checkConsistency Man page
GTR.getBaseFreqs Man page
GTR.getRateParam Man page
GTR.getRateParamList Man page
GTR.setBaseFreqs Man page
GTR.setRateParam Man page
GTR.setRateParamList Man page
GTR.summary Man page
GY94 Man page
GY94.checkConsistency Man page
GY94.getCodonFreqs Man page
GY94.getEventsAtSite Man page
GY94.getKappa Man page
GY94.getOmegaScalingFactor Man page
GY94.setCodonFreqs Man page
GY94.setKappa Man page
GY94.setRate Man page
GY94.summary Man page
hasSiteSpecificParameter Man page
hasSiteSpecificParameter.Process Man page
hasSiteSpecificParameter,Process-method Man page
hasSymbols Man page
hasSymbols.Alphabet Man page
hasSymbols,Alphabet-method Man page
hasUndefinedRate Man page
hasUndefinedRate.GeneralInDel Man page
hasUndefinedRate,GeneralInDel-method Man page
hasUndefinedRate.GeneralSubstitution Man page
hasUndefinedRate,GeneralSubstitution-method Man page
hasUndefinedRate.Process Man page
hasUndefinedRate,Process-method Man page
hasUndefinedRate.ToleranceSubstitution Man page
hasUndefinedRate,ToleranceSubstitution-method Man page
HKY Man page
HKY.checkConsistency Man page
HKY.getBaseFreqs Man page
HKY.getRateParam Man page
HKY.getRateParamList Man page
HKY.setBaseFreqs Man page
HKY.setRateParam Man page
HKY.setRateParamList Man page
HKY.summary Man page
insertSequence Man page
insertSequence.Sequence Man page
insertSequence,Sequence-method Man page
intersect Man page
intersect.list Man page
intersect.list.PSRoot Man page
intersect.list,PSRoot-method Man page
is Man page
is Man page
is.Alphabet Man page
is.Alphabet.default Man page
isAttached Man page
isAttached.Site Man page
isAttached,Site-method Man page
is.CodonAlphabet Man page
is.CodonAlphabet.default Man page
is.CodonUNREST Man page
is.CodonUNREST.default Man page
isEmpty Man page
isEmpty.Alphabet Man page
isEmpty,Alphabet-method Man page
is.Event Man page
is.Event.default Man page
is.GeneralDeletor Man page
is.GeneralDeletor.default Man page
is.GeneralInDel Man page
is.GeneralInDel.default Man page
is.GeneralInsertor Man page
is.GeneralInsertor.default Man page
is.GeneralSubstitution Man page
is.GeneralSubstitution.default Man page
is.GY94 Man page
is.GY94.default Man page
is.na.PSRoot Man page
is.na,PSRoot-method Man page
is.phylo Man page
is.phylo.default Man page
is.Process Man page
is.Process.default Man page
is.PSRoot Man page
is.PSRoot.default Man page
is.QMatrix Man page
is.QMatrix.default Man page
is.Sequence Man page
is.Sequence.default Man page
is.Site Man page
is.Site.default Man page
isStartCodon Man page
isStartCodon.CodonAlphabet Man page
isStartCodon,CodonAlphabet-method Man page
isStopCodon Man page
isStopCodon.CodonAlphabet Man page
isStopCodon,CodonAlphabet-method Man page
is.tip Man page
is.tip.PhyloSim Man page
is.tip,PhyloSim-method Man page
is.ToleranceSubstitution Man page
is.ToleranceSubstitution.default Man page
JC69 Man page
JC69.checkConsistency Man page
JC69.summary Man page
JTT Man page
JTT.dcmut Man page
K80 Man page
K80.checkConsistency Man page
K80.getBaseFreqs Man page
K80.getRateParam Man page
K80.getRateParamList Man page
K80.setBaseFreqs Man page
K80.setRateParam Man page
K80.setRateParamList Man page
K80.summary Man page
K81 Man page
K81.checkConsistency Man page
K81.getBaseFreqs Man page
K81.getRateParam Man page
K81.getRateParamList Man page
K81.setBaseFreqs Man page
K81.setRateParam Man page
K81.setRateParamList Man page
K81.summary Man page
LG Man page
list Man page
ll.PSRoot Man page
ll,PSRoot-method Man page
Log Man page
Log.PhyloSim Man page
Log,PhyloSim-method Man page
mtArt Man page
mtMam Man page
mtREV24 Man page
MtZoa Man page
my Man page
my.all.equal Man page
my.all.equal.PSRoot Man page
my.all.equal,PSRoot-method Man page
newAAMatrix Man page
newAAMatrix.AminoAcidSubst Man page
newAAMatrix,AminoAcidSubst-method Man page
newMatrix Man page
newMatrix.CodonSubst Man page
newMatrix,CodonSubst-method Man page
NucleotideAlphabet Man page
NucleotideSequence Man page
NucleotideSequence.revComp Man page
omegaHist Man page
omegaHist.CodonSequence Man page
omegaHist,CodonSequence-method Man page
omegaVarM0 Man page
omegaVarM0.CodonSequence Man page
omegaVarM0,CodonSequence-method Man page
omegaVarM1 Man page
omegaVarM10Cont Man page
omegaVarM10Cont Man page
omegaVarM1.CodonSequence Man page
omegaVarM1,CodonSequence-method Man page
omegaVarM2 Man page
omegaVarM2.CodonSequence Man page
omegaVarM2,CodonSequence-method Man page
omegaVarM3 Man page
omegaVarM3.CodonSequence Man page
omegaVarM3,CodonSequence-method Man page
omegaVarM4 Man page
omegaVarM4.CodonSequence Man page
omegaVarM4,CodonSequence-method Man page
PAM Man page
PAM.dcmut Man page
Perform Man page
Perform.Event Man page
Perform,Event-method Man page
phylosim Man page
PhyloSim Man page
PhyloSim.as.character Man page
PhyloSim.attachHookToNode Man page
PhyloSim.attachSeqToNode Man page
PhyloSim.checkConsistency Man page
PhyloSim.Debug Man page
PhyloSim.detachHookFromNode Man page
PhyloSim.detachSeqFromNode Man page
PhyloSim.exportStatTree Man page
PhyloSim.getAlignment Man page
PhyloSim.getAlignmentLength Man page
PhyloSim.getBranchEvents Man page
PhyloSim.getEdge Man page
PhyloSim.getEdges Man page
PhyloSim.getId Man page
PhyloSim.getLogFile Man page
PhyloSim.getLogLevel Man page
PhyloSim.getName Man page
PhyloSim.getNedges Man page
PhyloSim.getNodes Man page
PhyloSim.getNtips Man page
PhyloSim.getPhylo Man page
PhyloSim.getRootNode Man page
PhyloSim.getRootSeq Man page
PhyloSim.getSeqFromNode Man page
PhyloSim.getSequences Man page
PhyloSim.getTipLabels Man page
PhyloSim.getTips Man page
PhyloSim.getTreeLength Man page
PhyloSim.is.tip Man page
PhyloSim.Log Man page
PhyloSim.plot Man page
PhyloSim.readAlignment Man page
PhyloSim.readTree Man page
PhyloSim.saveAlignment Man page
PhyloSim.scaleTree Man page
PhyloSim.setAlignment Man page
PhyloSim.setBranchEvents Man page
PhyloSim.setEdges Man page
PhyloSim.setId Man page
PhyloSim.setLogFile Man page
PhyloSim.setLogLevel Man page
PhyloSim.setName Man page
PhyloSim.setNedges Man page
PhyloSim.setNodes Man page
PhyloSim.setNtips Man page
PhyloSim.setPhylo Man page
PhyloSim.setRootNode Man page
PhyloSim.setRootSeq Man page
PhyloSim.setSequences Man page
PhyloSim.setTipLabels Man page
PhyloSim.setTips Man page
PhyloSim.setTreeLength Man page
PhyloSim.Simulate Man page
PhyloSim.summary Man page
PhyloSim.Undocumented Man page
plot Man page
plot.ContinuousDeletor Man page
plot,ContinuousDeletor-method Man page
plot.ContinuousInsertor Man page
plot,ContinuousInsertor-method Man page
plot.DiscreteDeletor Man page
plot,DiscreteDeletor-method Man page
plot.DiscreteInsertor Man page
plot,DiscreteInsertor-method Man page
plot.GeneralSubstitution Man page
plot,GeneralSubstitution-method Man page
plotParametersAtSites Man page
plotParametersAtSites.Sequence Man page
plotParametersAtSites,Sequence-method Man page
plot.PhyloSim Man page
plot,PhyloSim-method Man page
plot.PSRoot Man page
plot.Sequence Man page
plot,Sequence-method Man page
plot.ToleranceSubstitution Man page
plot,ToleranceSubstitution-method Man page
plusGamma Man page
plusGamma.Sequence Man page
plusGamma,Sequence-method Man page
plusInvGamma Man page
plusInvGamma.Sequence Man page
plusInvGamma,Sequence-method Man page
print.PSRootSummary Man page
print,PSRootSummary-method Man page
print.QMatrix Man page
print,QMatrix-method Man page
Process Man page
==.Process Man page
!=.Process Man page
Process.== Man page
Process.as.character Man page
Process.checkConsistency Man page
Process.clone Man page
Process.getAlphabet Man page
Process.getEventsAtSite Man page
Process.getId Man page
Process.getName Man page
Process.getParameterAtSite Man page
Process.getSiteSpecificParamIds Man page
Process.getSiteSpecificParamList Man page
Process.getWriteProtected Man page
Process.hasSiteSpecificParameter Man page
Process.hasUndefinedRate Man page
==,Process-method Man page
Process.setAlphabet Man page
Process.setId Man page
Process.setName Man page
Process.setParameterAtSite Man page
Process.setSiteSpecificParamIds Man page
Process.setSiteSpecificParamList Man page
Process.setWriteProtected Man page
Process.summary Man page
proposeLength Man page
proposeLength.GeneralInDel Man page
proposeLength,GeneralInDel-method Man page
PSRoot Man page
PSRoot.checkConsistency Man page
PSRoot.enableVirtual Man page
PSRoot.getComments Man page
PSRoot.getMethodsList Man page
PSRoot.globalConsistencyCheck Man page
PSRoot.intersect.list Man page
PSRoot.is.na Man page
PSRoot.ll Man page
PSRoot.my.all.equal Man page
PSRoot.setComments Man page
PSRoot.setMethodsList Man page
PSRoot.summary Man page
PSRootSummary Man page
PSRootSummary.checkConsistency Man page
PSRootSummary.print Man page
PSRoot.virtualAssignmentForbidden Man page
QMatrix Man page
QMatrix.as.character Man page
QMatrix.checkConsistency Man page
QMatrix.getAlphabet Man page
QMatrix.getEventRate Man page
QMatrix.getId Man page
QMatrix.getMatrix Man page
QMatrix.getName Man page
QMatrix.getProcess Man page
QMatrix.getRate Man page
QMatrix.getRateList Man page
QMatrix.getScaledMatrix Man page
QMatrix.getWriteProtected Man page
QMatrix.print Man page
QMatrix.Scale Man page
QMatrix.setAlphabet Man page
QMatrix.setId Man page
QMatrix.setMatrix Man page
QMatrix.setName Man page
QMatrix.setProcess Man page
QMatrix.setRate Man page
QMatrix.setRateList Man page
QMatrix.setScaledMatrix Man page
QMatrix.setWriteProtected Man page
QMatrix.summary Man page
readAlignment Man page
readAlignment.PhyloSim Man page
readAlignment,PhyloSim-method Man page
readTree Man page
readTree.PhyloSim Man page
readTree,PhyloSim-method Man page
rescaleQMatrix Man page
rescaleQMatrix.GeneralSubstitution Man page
rescaleQMatrix,GeneralSubstitution-method Man page
rescaleQMatrix.ToleranceSubstitution Man page
rescaleQMatrix,ToleranceSubstitution-method Man page
revComp Man page
revComp.NucleotideSequence Man page
revComp,NucleotideSequence-method Man page
sampleState Man page
sampleState.GeneralSubstitution Man page
sampleState,GeneralSubstitution-method Man page
sampleStates Man page
sampleStates.Sequence Man page
sampleStates,Sequence-method Man page
sampleState.ToleranceSubstitution Man page
sampleState,ToleranceSubstitution-method Man page
saveAlignment Man page
saveAlignment.PhyloSim Man page
saveAlignment,PhyloSim-method Man page
saveLoadReference Man page
Scale Man page
Scale.QMatrix Man page
Scale,QMatrix-method Man page
scaleTree Man page
scaleTree.PhyloSim Man page
scaleTree,PhyloSim-method Man page
Sequence Man page
Sequence.as.character Man page
Sequence.attachProcess Man page
Sequence.checkConsistency Man page
Sequence.clearStates Man page
Sequence.clone Man page
Sequence.copySubSequence Man page
Sequence.deleteSubSequence Man page
Sequence.detachProcess Man page
Sequence.getAlphabets Man page
Sequence.getAncestral Man page
Sequence.getBigRate Man page
Sequence.getCumulativeRates Man page
Sequence.getCumulativeRatesFromRange Man page
Sequence.getDeletionTolerance Man page
Sequence.getEvents Man page
Sequence.getId Man page
Sequence.getInsertionTolerance Man page
Sequence.getLength Man page
Sequence.getName Man page
Sequence.getParameterAtSites Man page
Sequence.getProcesses Man page
Sequence.getRateMultipliers Man page
Sequence.getSites Man page
Sequence.getStates Man page
Sequence.getString Man page
Sequence.getSymbolFreqs Man page
Sequence.getTotalRates Man page
Sequence.getTotalRatesFromRange Man page
Sequence.getUniqueAlphabets Man page
Sequence.getUniqueProcesses Man page
Sequence.getWriteProtected Man page
Sequence.insertSequence Man page
Sequence.plot Man page
Sequence.plotParametersAtSites Man page
Sequence.plusGamma Man page
Sequence.plusInvGamma Man page
Sequence.sampleStates Man page
Sequence.setAlphabets Man page
Sequence.setAncestral Man page
Sequence.setBigRate Man page
Sequence.setCumulativeRates Man page
Sequence.setDeletionTolerance Man page
Sequence.setId Man page
Sequence.setInsertionTolerance Man page
Sequence.setLength Man page
Sequence.setName Man page
Sequence.setParameterAtSites Man page
Sequence.setProcesses Man page
Sequence.setRateMultipliers Man page
Sequence.setStates Man page
Sequence.setString Man page
Sequence.setTotalRates Man page
Sequence.setUniqueAlphabets Man page
Sequence.setUniqueProcesses Man page
Sequence.setWriteProtected Man page
Sequence.summary Man page
setAcceptBy Man page
setAcceptBy.GeneralInDel Man page
setAcceptBy,GeneralInDel-method Man page
setAcceptBy.GeneralInsertor Man page
setAcceptWin Man page
setAcceptWin.GeneralInsertor Man page
setAcceptWin,GeneralInsertor-method Man page
setAlignment Man page
setAlignment.PhyloSim Man page
setAlignment,PhyloSim-method Man page
setAlphabet Man page
setAlphabet.GeneralSubstitution Man page
setAlphabet,GeneralSubstitution-method Man page
setAlphabet.Process Man page
setAlphabet,Process-method Man page
setAlphabet.QMatrix Man page
setAlphabet,QMatrix-method Man page
setAlphabets Man page
setAlphabet.Site Man page
setAlphabet,Site-method Man page
setAlphabets.Sequence Man page
setAlphabets,Sequence-method Man page
setAlphabet.ToleranceSubstitution Man page
setAlphabet,ToleranceSubstitution-method Man page
setAncestral Man page
setAncestral.Sequence Man page
setAncestral,Sequence-method Man page
setAncestral.Site Man page
setAncestral,Site-method Man page
setBaseFreqs Man page
setBaseFreqs.F81 Man page
setBaseFreqs,F81-method Man page
setBaseFreqs.F84 Man page
setBaseFreqs,F84-method Man page
setBaseFreqs.GTR Man page
setBaseFreqs,GTR-method Man page
setBaseFreqs.HKY Man page
setBaseFreqs,HKY-method Man page
setBaseFreqs.K80 Man page
setBaseFreqs,K80-method Man page
setBaseFreqs.K81 Man page
setBaseFreqs,K81-method Man page
setBaseFreqs.TN93 Man page
setBaseFreqs,TN93-method Man page
setBigRate Man page
setBigRate.Sequence Man page
setBigRate,Sequence-method Man page
setBranchEvents Man page
setBranchEvents.PhyloSim Man page
setBranchEvents,PhyloSim-method Man page
setCodonFreqs Man page
setCodonFreqs Man page
setCodonFreqs.GY94 Man page
setCodonFreqs,GY94-method Man page
setComments Man page
setComments.PSRoot Man page
setComments,PSRoot-method Man page
setCumulativeRates Man page
setCumulativeRates.Sequence Man page
setCumulativeRates,Sequence-method Man page
setDeletionTolerance Man page
setDeletionTolerance.Sequence Man page
setDeletionTolerance,Sequence-method Man page
setDist Man page
setDist.ContinuousDeletor Man page
setDist,ContinuousDeletor-method Man page
setDist.ContinuousInsertor Man page
setDist,ContinuousInsertor-method Man page
setEdges Man page
setEdges.PhyloSim Man page
setEdges,PhyloSim-method Man page
setEquDist Man page
setEquDist Man page
setEquDist.AminoAcidSubst Man page
setEquDist.CodonSubst Man page
setEquDist.GeneralSubstitution Man page
setEquDist,GeneralSubstitution-method Man page
setEquDist.ToleranceSubstitution Man page
setEquDist,ToleranceSubstitution-method Man page
setEvents Man page
setEvents.Site Man page
setEvents,Site-method Man page
setGenerateBy Man page
setGenerateBy.GeneralInsertor Man page
setGenerateBy,GeneralInsertor-method Man page
setHandler Man page
setHandler.Event Man page
setHandler,Event-method Man page
setId Man page
setId.PhyloSim Man page
setId,PhyloSim-method Man page
setId.Process Man page
setId,Process-method Man page
setId.QMatrix Man page
setId,QMatrix-method Man page
setId.Sequence Man page
setId,Sequence-method Man page
setInsertHook Man page
setInsertHook.GeneralInsertor Man page
setInsertHook,GeneralInsertor-method Man page
setInsertionTolerance Man page
setInsertionTolerance Man page
setInsertionTolerance.Sequence Man page
setInsertionTolerance,Sequence-method Man page
setKappa Man page
setKappa Man page
setKappa.F84 Man page
setKappa,F84-method Man page
setKappa.GY94 Man page
setKappa,GY94-method Man page
setLength Man page
setLengthParam1 Man page
setLengthParam1.FastFieldDeletor Man page
setLengthParam1,FastFieldDeletor-method Man page
setLengthParam2 Man page
setLengthParam2.FastFieldDeletor Man page
setLengthParam2,FastFieldDeletor-method Man page
setLength.Sequence Man page
setLength,Sequence-method Man page
setLogFile Man page
setLogFile.PhyloSim Man page
setLogFile,PhyloSim-method Man page
setLogLevel Man page
setLogLevel.PhyloSim Man page
setLogLevel,PhyloSim-method Man page
setMatrix Man page
setMatrix.QMatrix Man page
setMatrix,QMatrix-method Man page
setMaxLength Man page
setMaxLength.ContinuousDeletor Man page
setMaxLength,ContinuousDeletor-method Man page
setMaxLength.ContinuousInsertor Man page
setMaxLength,ContinuousInsertor-method Man page
setMethodsList Man page
setMethodsList.PSRoot Man page
setMethodsList,PSRoot-method Man page
setName Man page
setName.Event Man page
setName,Event-method Man page
setName.PhyloSim Man page
setName,PhyloSim-method Man page
setName.Process Man page
setName,Process-method Man page
setName.QMatrix Man page
setName,QMatrix-method Man page
setName.Sequence Man page
setName,Sequence-method Man page
setNedges Man page
setNedges.PhyloSim Man page
setNedges,PhyloSim-method Man page
setNodes Man page
setNodes.PhyloSim Man page
setNodes,PhyloSim-method Man page
setNtips Man page
setNtips.PhyloSim Man page
setNtips,PhyloSim-method Man page
setOmegas Man page
setOmegas.CodonSequence Man page
setOmegas,CodonSequence-method Man page
setOmegas.Sequence Man page
setParameterAtSite Man page
setParameterAtSite.FastFieldDeletor Man page
setParameterAtSite.Process Man page
setParameterAtSite,Process-method Man page
setParameterAtSites Man page
setParameterAtSites.Sequence Man page
setParameterAtSites,Sequence-method Man page
setPhylo Man page
setPhylo.PhyloSim Man page
setPhylo,PhyloSim-method Man page
setPosition Man page
setPosition.Event Man page
setPosition,Event-method Man page
setProbs Man page
setProbs.DiscreteDeletor Man page
setProbs,DiscreteDeletor-method Man page
setProbs.DiscreteInsertor Man page
setProbs,DiscreteInsertor-method Man page
setProcess Man page
setProcesses Man page
setProcesses.Sequence Man page
setProcesses,Sequence-method Man page
setProcesses.Site Man page
setProcesses,Site-method Man page
setProcess.Event Man page
setProcess,Event-method Man page
setProcess.QMatrix Man page
setProcess,QMatrix-method Man page
setProposeBy Man page
setProposeBy.GeneralInDel Man page
setProposeBy,GeneralInDel-method Man page
setProposeBy.GeneralInsertor Man page
setQMatrix Man page
setQMatrix.GeneralSubstitution Man page
setQMatrix,GeneralSubstitution-method Man page
setQMatrix.ToleranceSubstitution Man page
setQMatrix,ToleranceSubstitution-method Man page
setRate Man page
setRate.Event Man page
setRate,Event-method Man page
setRate.GeneralInDel Man page
setRate,GeneralInDel-method Man page
setRate.GeneralSubstitution Man page
setRate,GeneralSubstitution-method Man page
setRate.GY94 Man page
setRate,GY94-method Man page
setRateList Man page
setRateList.GeneralSubstitution Man page
setRateList,GeneralSubstitution-method Man page
setRateList.QMatrix Man page
setRateList,QMatrix-method Man page
setRateList.ToleranceSubstitution Man page
setRateList,ToleranceSubstitution-method Man page
setRateMultipliers Man page
setRateMultipliers.Sequence Man page
setRateMultipliers,Sequence-method Man page
setRateParam Man page
setRateParam.F81 Man page
setRateParam,F81-method Man page
setRateParam.F84 Man page
setRateParam,F84-method Man page
setRateParam.GTR Man page
setRateParam,GTR-method Man page
setRateParam.HKY Man page
setRateParam,HKY-method Man page
setRateParam.K80 Man page
setRateParam,K80-method Man page
setRateParam.K81 Man page
setRateParam,K81-method Man page
setRateParamList Man page
setRateParamList.F81 Man page
setRateParamList,F81-method Man page
setRateParamList.F84 Man page
setRateParamList,F84-method Man page
setRateParamList.GTR Man page
setRateParamList,GTR-method Man page
setRateParamList.HKY Man page
setRateParamList,HKY-method Man page
setRateParamList.K80 Man page
setRateParamList,K80-method Man page
setRateParamList.K81 Man page
setRateParamList,K81-method Man page
setRateParamList.T92 Man page
setRateParamList,T92-method Man page
setRateParamList.TN93 Man page
setRateParamList,TN93-method Man page
setRateParam.T92 Man page
setRateParam,T92-method Man page
setRateParam.TN93 Man page
setRateParam,TN93-method Man page
setRate.QMatrix Man page
setRate,QMatrix-method Man page
setRate.ToleranceSubstitution Man page
setRate,ToleranceSubstitution-method Man page
setRootNode Man page
setRootNode.PhyloSim Man page
setRootNode,PhyloSim-method Man page
setRootSeq Man page
setRootSeq.PhyloSim Man page
setRootSeq,PhyloSim-method Man page
setScale Man page
setScale.BrownianInsertor Man page
setScale,BrownianInsertor-method Man page
setScaledMatrix Man page
setScaledMatrix.QMatrix Man page
setScaledMatrix,QMatrix-method Man page
setSequence Man page
setSequences Man page
setSequence.Site Man page
setSequence,Site-method Man page
setSequences.PhyloSim Man page
setSequences,PhyloSim-method Man page
setSite Man page
setSite.Event Man page
setSite,Event-method Man page
setSiteSpecificParamIds Man page
setSiteSpecificParamIds.Process Man page
setSiteSpecificParamIds,Process-method Man page
setSiteSpecificParamList Man page
setSiteSpecificParamList.Process Man page
setSiteSpecificParamList,Process-method Man page
setSize Man page
setSize.Alphabet Man page
setSize,Alphabet-method Man page
setSizes Man page
setSizes.DiscreteDeletor Man page
setSizes,DiscreteDeletor-method Man page
setSizes.DiscreteInsertor Man page
setSizes,DiscreteInsertor-method Man page
setState Man page
setStates Man page
setState.Site Man page
setState,Site-method Man page
setStates.Sequence Man page
setStates,Sequence-method Man page
setString Man page
setString.Sequence Man page
setString,Sequence-method Man page
setSymbolLength Man page
setSymbolLength.Alphabet Man page
setSymbolLength,Alphabet-method Man page
setSymbols Man page
setSymbols.Alphabet Man page
setSymbols,Alphabet-method Man page
setTableId Man page
setTableId.CodonAlphabet Man page
setTableId,CodonAlphabet-method Man page
setTargetState Man page
setTemplateSeq Man page
setTemplateSeq.GeneralInsertor Man page
setTemplateSeq,GeneralInsertor-method Man page
setTheta Man page
setTheta.T92 Man page
setTheta,T92-method Man page
setTipLabels Man page
setTipLabels.PhyloSim Man page
setTipLabels,PhyloSim-method Man page
setTips Man page
setTips.PhyloSim Man page
setTips,PhyloSim-method Man page
setToleranceMargin Man page
setToleranceMargin.FastFieldDeletor Man page
setToleranceMargin,FastFieldDeletor-method Man page
setTotalRate Man page
setTotalRates Man page
setTotalRate.Site Man page
setTotalRate,Site-method Man page
setTotalRates.Sequence Man page
setTotalRates,Sequence-method Man page
setTransTable Man page
setTransTable.CodonAlphabet Man page
setTransTable,CodonAlphabet-method Man page
setTreeLength Man page
setTreeLength.PhyloSim Man page
setTreeLength,PhyloSim-method Man page
setType Man page
setType.Alphabet Man page
setType,Alphabet-method Man page
setType.BrownianInsertor Man page
setType,BrownianInsertor-method Man page
setType.FastFieldDeletor Man page
setType,FastFieldDeletor-method Man page
setUniqueAlphabets Man page
setUniqueAlphabets.Sequence Man page
setUniqueAlphabets,Sequence-method Man page
setUniqueProcesses Man page
setUniqueProcesses.Sequence Man page
setUniqueProcesses,Sequence-method Man page
setWriteProtected Man page
setWriteProtected.Alphabet Man page
setWriteProtected,Alphabet-method Man page
setWriteProtected.Event Man page
setWriteProtected,Event-method Man page
setWriteProtected.Process Man page
setWriteProtected,Process-method Man page
setWriteProtected.QMatrix Man page
setWriteProtected,QMatrix-method Man page
setWriteProtected.Sequence Man page
setWriteProtected,Sequence-method Man page
Simulate Man page
Simulate.PhyloSim Man page
Simulate,PhyloSim-method Man page
Site Man page
Site.as.character Man page
Site.attachProcess Man page
Site.checkConsistency Man page
Site.detachProcess Man page
Site.flagTotalRate Man page
Site.getAlphabet Man page
Site.getAncestral Man page
Site.getEvents Man page
Site.getProcesses Man page
Site.getSequence Man page
Site.getState Man page
Site.getTotalRate Man page
Site.isAttached Man page
Site.setAlphabet Man page
Site.setAncestral Man page
Site.setEvents Man page
Site.setProcesses Man page
Site.setSequence Man page
Site.setState Man page
Site.setTotalRate Man page
Site.summary Man page
stringLength Man page
stringLength.default Man page
stringLengthVector Man page
stringLengthVector.default Man page
summary.Alphabet Man page
summary,Alphabet-method Man page
summary.AminoAcidSubst Man page
summary,AminoAcidSubst-method Man page
summary.BinarySubst Man page
summary,BinarySubst-method Man page
summary.BrownianInsertor Man page
summary,BrownianInsertor-method Man page
summary.CodonAlphabet Man page
summary,CodonAlphabet-method Man page
summary.CodonSubst Man page
summary,CodonSubst-method Man page
summary.ContinuousDeletor Man page
summary,ContinuousDeletor-method Man page
summary.ContinuousInsertor Man page
summary,ContinuousInsertor-method Man page
summary.DiscreteDeletor Man page
summary,DiscreteDeletor-method Man page
summary.DiscreteInsertor Man page
summary,DiscreteInsertor-method Man page
summary.Event Man page
summary,Event-method Man page
summary.F81 Man page
summary,F81-method Man page
summary.F84 Man page
summary,F84-method Man page
summary.FastFieldDeletor Man page
summary,FastFieldDeletor-method Man page
summary.GeneralDeletor Man page
summary,GeneralDeletor-method Man page
summary.GeneralInDel Man page
summary,GeneralInDel-method Man page
summary.GeneralInsertor Man page
summary,GeneralInsertor-method Man page
summary.GeneralSubstitution Man page
summary,GeneralSubstitution-method Man page
summary.GTR Man page
summary,GTR-method Man page
summary.GY94 Man page
summary,GY94-method Man page
summary.HKY Man page
summary,HKY-method Man page
summary.JC69 Man page
summary,JC69-method Man page
summary.K80 Man page
summary,K80-method Man page
summary.K81 Man page
summary,K81-method Man page
summary.PhyloSim Man page
summary,PhyloSim-method Man page
summary.Process Man page
summary,Process-method Man page
summary.PSRoot Man page
summary,PSRoot-method Man page
summary.QMatrix Man page
summary,QMatrix-method Man page
summary.Sequence Man page
summary,Sequence-method Man page
summary.Site Man page
summary,Site-method Man page
summary.T92 Man page
summary,T92-method Man page
summary.TN93 Man page
summary,TN93-method Man page
summary.ToleranceSubstitution Man page
summary,ToleranceSubstitution-method Man page
summary.UNREST Man page
summary,UNREST-method Man page
T92 Man page
T92.checkConsistency Man page
T92.getRateParam Man page
T92.getRateParamList Man page
T92.getTheta Man page
T92.setRateParam Man page
T92.setRateParamList Man page
T92.setTheta Man page
T92.summary Man page
tip Man page
TN93 Man page
TN93.checkConsistency Man page
TN93.getBaseFreqs Man page
TN93.getRateParam Man page
TN93.getRateParamList Man page
TN93.setBaseFreqs Man page
TN93.setRateParam Man page
TN93.setRateParamList Man page
TN93.summary Man page
ToleranceSubstitution Man page
ToleranceSubstitution.as.character Man page
ToleranceSubstitution.checkConsistency Man page
ToleranceSubstitution.clone Man page
ToleranceSubstitution.getAlphabet Man page
ToleranceSubstitution.getEquDist Man page
ToleranceSubstitution.getEventRate Man page
ToleranceSubstitution.getEventRateAtSite Man page
ToleranceSubstitution.getEventsAtSite Man page
ToleranceSubstitution.getQMatrix Man page
ToleranceSubstitution.getRate Man page
ToleranceSubstitution.getRateList Man page
ToleranceSubstitution.hasUndefinedRate Man page
ToleranceSubstitution.plot Man page
ToleranceSubstitution.rescaleQMatrix Man page
ToleranceSubstitution.sampleState Man page
ToleranceSubstitution.setAlphabet Man page
ToleranceSubstitution.setEquDist Man page
ToleranceSubstitution.setQMatrix Man page
ToleranceSubstitution.setRate Man page
ToleranceSubstitution.setRateList Man page
ToleranceSubstitution.summary Man page
Translate Man page
translateCodon Man page
translateCodon.CodonAlphabet Man page
translateCodon,CodonAlphabet-method Man page
Translate.CodonSequence Man page
Translate,CodonSequence-method Man page
Undocumented Man page
Undocumented.PhyloSim Man page
Undocumented,PhyloSim-method Man page
UNREST Man page
UNREST.checkConsistency Man page
UNREST.summary Man page
virtualAssignmentForbidden Man page
virtualAssignmentForbidden.PSRoot Man page
virtualAssignmentForbidden,PSRoot-method Man page
WAG Man page

Files

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 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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 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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 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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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