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.

Author
Botond Sipos <sbotond@gmail.com>, Gregory Jordan <greg@ebi.ac.uk>
Date of publication
2016-09-08 20:14:57
Maintainer
Botond Sipos <sbotond@gmail.com>
License
GPL (>= 3)
Version
3.0.2
URLs

View on CRAN

Man pages

000==.Alphabet
Check if two alaphabet objects have the same symbol set
000==.Process
Check whether the two supplied Process objects are identical
Alphabet
The Alphabet class
AminoAcidAlphabet
The AminoAcidAlphabet class
AminoAcidSequence
The AminoAcidSequence class
AminoAcidSubst
The AminoAcidSubst class
AnyAlphabet
The AnyAlphabet class
areSynonymous.CodonAlphabet
Check whether two codons are synonymous
as.character.Alphabet
Get the character representation of an Alphabet object
as.character.Event
Get the character representation of an Event object
as.character.GeneralSubstitution
Return the character representation of a GeneralSubstitution...
as.character.PhyloSim
Return the character representation of a PhyloSim object
as.character.Process
Get the character representation of a Process object
as.character.QMatrix
Return the character representation of a QMatrix object
as.character.Sequence
Get the string representation of a Sequence object
as.character.Site
Get the character representation of a Site object
as.character.ToleranceSubstitution
Return the character representation of a...
attachHookToNode.PhyloSim
Attach a callback function to a given node of a phylo object...
attachProcess.Sequence
Attach a Process object to a set of Site objects aggregated...
attachProcess.Site
Attach a Process object to a Site object
attachSeqToNode.PhyloSim
Assotiate a Sequence object with a given node of a phylo...
BinaryAlphabet
The BinaryAlphabet class
BinarySequence
The BinarySequence class
BinarySubst
The BinarySubst class
BrownianInsertor
The BrownianInsertor class
BrownianPath.BrownianInsertor
Generate a Brownian path
buildFromPAML.AminoAcidSubst
Build rate matrix from PAML file
buildFromPAML.CodonSubst
Build rate matrix from PAML file
checkConsistency.Alphabet
Check object consistency
checkConsistency.AminoAcidSubst
Check object consistency
checkConsistency.BinarySubst
Check object consistency
checkConsistency.BrownianInsertor
Check object consistency
checkConsistency.CodonAlphabet
Check object consistency
checkConsistency.CodonSequence
Check object consistency
checkConsistency.CodonSubst
Check object consistency
checkConsistency.CodonUNREST
Check object consistency
checkConsistency.ContinuousDeletor
Check object consistency
checkConsistency.ContinuousInsertor
Check object consistency
checkConsistency.DiscreteDeletor
Check object consistency
checkConsistency.DiscreteInsertor
Check object consistency
checkConsistency.Event
Check object consistency
checkConsistency.F81
Check object consistency
checkConsistency.F84
Check object consistency
checkConsistency.FastFieldDeletor
Check object consistency
checkConsistency.GeneralDeletor
Check object consistency
checkConsistency.GeneralInDel
Check object consistency
checkConsistency.GeneralInsertor
Check object consistency
checkConsistency.GeneralSubstitution
Check object consistency
checkConsistency.GTR
Check object consistency
checkConsistency.GY94
Check object consistency
checkConsistency.HKY
Check object consistency
checkConsistency.JC69
Check object consistency
checkConsistency.K80
Check object consistency
checkConsistency.K81
Check object consistency
checkConsistency.PhyloSim
Check object consistency
checkConsistency.Process
Check object consistency
checkConsistency.PSRoot
Check object consistency
checkConsistency.PSRootSummary
Check object consistency
checkConsistency.QMatrix
Check object consistency
checkConsistency.Sequence
Check object consistency
checkConsistency.Site
Check object consistency
checkConsistency.T92
Check object consistency
checkConsistency.TN93
Check object consistency
checkConsistency.ToleranceSubstitution
Check object consistency
checkConsistency.UNREST
Check object consistency
clearStates.Sequence
Set the states of a collection of Site objects aggregated by...
clone.GeneralSubstitution
Clone a GeneralSubstitution object
clone.Process
Clone a process object
clone.Sequence
Clone a Sequence object
clone.ToleranceSubstitution
Clone a ToleranceSubstitution object
CodonAlphabet
The CodonAlphabet class
CodonSequence
The CodonSequence class
CodonSubst
The CodonSubst class
CodonUNREST
The CodonUNREST class
ContinuousDeletor
The ContinuousDeletor class
ContinuousInsertor
The ContinuousInsertor class
copySubSequence.Sequence
Copy a collection of Site objects aggregated by a Sequence...
cpREV
The cpREV empirical amino acid substitution model
Debug.PhyloSim
Save a debug message in the PhyloSim log file
deleteSubSequence.Sequence
Delete a collection of sites aggregated by a Sequence object
detachHookFromNode.PhyloSim
Detach a node hook function from a given node of a phylo...
detachProcess.Sequence
Detach a Process object from a set of Site objects aggregated...
detachProcess.Site
Site
detachSeqFromNode.PhyloSim
Detach a Sequence object from a given node of a phylo object...
DiscreteDeletor
The DiscreteDeletor class
DiscreteInsertor
The DiscreteInsertor class
ECMrest
The ECMrest empirical codon substitution model
ECMunrest
The ECMunrest empirical codon substitution model
enableVirtual.PSRoot
Enable the use of virtual fields for a given object
Event
The Event class
exportStatTree.PhyloSim
Export the per-branch counts of an event as a phylo object
F81
The F81 class
F84
The F84 class
FastFieldDeletor
The FastFieldDeletor class
flagTotalRate.Site
Flag the total event rate
GeneralDeletor
The GeneralDeletor class
GeneralInDel
The GeneralInDel class
GeneralInsertor
The GeneralInsertor class
GeneralSubstitution
The GeneralSubstitution class
generateInsert.GeneralInsertor
Generate an insert
getAcceptBy.GeneralInDel
Get the function used for accepting/rejecting indel events
getAcceptWin.GeneralInsertor
Get the size of the acceptance window
getAlignmentLength.PhyloSim
Get the alignment length from a PhyloSim object
getAlignment.PhyloSim
Get the alignment stored in a PhyloSim object
getAlphabet.GeneralSubstitution
Get the Alphabet object aggregated by a GeneralSubstitution...
getAlphabet.Process
Get the Alphabet object associated with a given Process...
getAlphabet.QMatrix
Get the Alphabet object associated with a QMatrix object
getAlphabet.Site
Get the Alphabet object attached to a Site object
getAlphabets.Sequence
Get the list of the Alphabet objects attached to the Site...
getAlphabet.ToleranceSubstitution
Get the Alphabet object aggregated by a ToleranceSubstitution...
getAncestral.Sequence
Get the ancestral object of a Sequence object
getAncestral.Site
Get the ancestral object of a Site object
getBaseFreqs.F81
Get the base frequency parameters
getBaseFreqs.F84
Get the base frequency parameters
getBaseFreqs.GTR
Get the base frequency parameters
getBaseFreqs.HKY
Get the base frequency parameters
getBaseFreqs.K80
Get the base frequency parameters
getBaseFreqs.K81
Get the base frequency parameters
getBaseFreqs.TN93
Get the base frequency parameters
getBigRate.Sequence
Get the sum of all active event rates from a Sequence object
getBranchEvents.PhyloSim
Get the list of events having per-branch statistics recorded
getCodonFreqs.GY94
Get codon frequencies
getComments.PSRoot
Get the comments associated with an object
getCumulativeRatesFromRange.Sequence
Get the cumulative site rates for a collection of Site...
getCumulativeRates.Sequence
Get the total site rates from a Sequence object
getDeletionTolerance.Sequence
Get the deletion tolerance site-process specific parameter...
getDist.ContinuousDeletor
Get the length sampling expression
getDist.ContinuousInsertor
Get the length sampling expression
getEdge.PhyloSim
Get and edge from the edge matrix
getEdges.PhyloSim
Get the edge matrix from a phylo object aggregated by a...
getEquDist.GeneralSubstitution
Get the equilibrium distribution from a GeneralSubstitution...
getEquDist.ToleranceSubstitution
Get the equilibrium distribution from a ToleranceSubstitution...
getEventRateAtSite.GeneralSubstitution
Get the site spcific rate of an event from a...
getEventRateAtSite.ToleranceSubstitution
Get the site spcific rate of an event from a...
getEventRate.GeneralSubstitution
Get the scaled rate of an event from a GeneralSubstitution...
getEventRate.QMatrix
Get the unscaled rate of an event from a QMatrix object
getEventRate.ToleranceSubstitution
Get the scaled rate of an event from a ToleranceSubstitution...
getEventsAtSite.FastFieldDeletor
Generate a deletion event object given the state of the...
getEventsAtSite.GeneralDeletor
Title
getEventsAtSite.GeneralInsertor
Generate insertion event object given the state of the target...
getEventsAtSite.GeneralSubstitution
Generate the list of active Event objects for a given...
getEventsAtSite.GY94
Generate the list of active Event objects for a given...
getEventsAtSite.Process
Generate the list of active Event objects given a Site object
getEventsAtSite.ToleranceSubstitution
Generate the list of active Event objects for a given...
getEvents.Sequence
Get the list of active Event objects for a set of Site...
getEvents.Site
Get the list of active event objects given the current state...
getGenerateBy.GeneralInsertor
Get the function object used for generating inserts
getHandler.Event
Get the handler function of an Event object
getId.PhyloSim
Get the unique identifier of a PhyloSim object
getId.Process
Get the unique identifier of a Process object
getId.QMatrix
Get the unique identifier of a QMatrix object
getId.Sequence
Get the unique identifier of a Sequence object
getInsertHook.GeneralInsertor
Get the insert hook function
getInsertionTolerance.Sequence
Get the insertion tolerance site-process specific parameter...
getKappa.F84
Get the transition transversion rate ratio
getKappa.GY94
Get the transition/transversion rate ratio
getLengthParam1.FastFieldDeletor
Get the first length parameter
getLengthParam2.FastFieldDeletor
Get the second length parameter
getLength.Sequence
Get the number of Site objects aggregated in a Sequence...
getLogFile.PhyloSim
Get the name of the file used for logging
getLogLevel.PhyloSim
Get the log level from a PhyloSim object
getMatrix.QMatrix
Get the unscaled rate matrix form a QMatrix object
getMaxLength.ContinuousDeletor
Get the maximum length
getMaxLength.ContinuousInsertor
Get the maximum length
getMethodsList.PSRoot
Get the list of applicable methods for an object
getName.Event
Get the name of an Event object
getName.PhyloSim
Get the name of a PhyloSim object
getName.Process
Get the name of a Process object
getName.QMatrix
Get the name of a QMatrix object
getName.Sequence
Get the name of a Sequence object
getNedges.PhyloSim
Get the number of edges from phylo object aggregated by a...
getNodes.PhyloSim
Get the node identifiers from a PhyloSim object
getNtips.PhyloSim
Get the number of the tips form a phylo object aggregated by...
getOmegaScalingFactor.GY94
Get the omega scaling factor
getOmegas.CodonSequence
Get the omegas from a collection of sites
getParameterAtSite.Process
Get the value of a site-process specific paramter from a Site...
getParameterAtSites.Sequence
Get the values of a site-process specific paramater for a...
getPhylo.PhyloSim
Get the phylo object aggregated in a PhyloSim object
getPosition.Event
Get the position of the Site object associated to an Event...
getProbs.DiscreteDeletor
Get the deletion length probabilities
getProbs.DiscreteInsertor
Get the insertion length probabilities
getProcesses.Sequence
Get the Process objects attached to the Site objects...
getProcesses.Site
Get the list of Process objects attached to a Site object
getProcess.Event
Get the Process object which generated an Event object
getProcess.QMatrix
Get the process object associated with a QMatrix object
getProposeBy.GeneralInDel
Get the function used for proposing indel lengths
getQMatrix.GeneralSubstitution
Get the QMatrix object aggregated by a GeneralSubstitution...
getQMatrix.ToleranceSubstitution
Get the QMatrix object aggregated by a ToleranceSubstitution...
getRate.Event
Get the rate of an Event object
getRate.GeneralInDel
Get the general rate
getRate.GeneralSubstitution
Get an unscaled rate of an event from a GeneralSubstitution...
getRateList.GeneralSubstitution
Get a list of events and their unscaled rates from a...
getRateList.QMatrix
Get a list of events and their unscaled rates from a QMatrix...
getRateList.ToleranceSubstitution
Get a list of events and their unscaled rates from a...
getRateMultipliers.Sequence
Get the values of the rate multiplier parameters for a given...
getRateParam.F81
Forbidden action: the value of a rate parameters
getRateParam.F84
Get the value of a rate parameter
getRateParam.GTR
Get the value of a rate parameter
getRateParam.HKY
Get the value of a rate parameter
getRateParam.K80
Get the value of a rate parameter
getRateParam.K81
Get the value of a rate parameter
getRateParamList.F81
Forbidden action: getting the list of rate parameters
getRateParamList.F84
Get the rate parameters
getRateParamList.GTR
Get the rate parameters
getRateParamList.HKY
Get the rate parameters
getRateParamList.K80
Get the rate parameters
getRateParamList.K81
Get the rate parameters
getRateParamList.T92
Get the rate parameters
getRateParamList.TN93
Get the rate parameters
getRateParam.T92
Get the value of a rate parameter
getRateParam.TN93
Get the value of a rate parameter
getRate.QMatrix
Get an unscaled rate of an event from a QMatrix object
getRate.ToleranceSubstitution
Get an unscaled rate of an event from a ToleranceSubstitution...
getRootNode.PhyloSim
Get the identifier of the root node from a PhyloSim object
getRootSeq.PhyloSim
Get the root sequence aggregated by a PhyloSim object
getScale.BrownianInsertor
Get scale parameter
getScaledMatrix.QMatrix
Get the scaled rate matrix form a QMatrix object
getSeqFromNode.PhyloSim
Get the Sequence object associated with a given node of a...
getSequence.Site
Get the Sequence object associated with a given Site object
getSequences.PhyloSim
Gets all the Sequence objects associated with the nodes of a...
getSite.Event
Get the Site object associated with an Event object
getSiteSpecificParamIds.Process
Get the site specific paramter identifiers from a Process...
getSiteSpecificParamList.Process
Get the list of site specific parameters of a Process object
getSites.Sequence
Get the list of the Site object aggregated in a Sequence...
getSize.Alphabet
Get the number of symbols in an Alphabet object
getSizes.DiscreteDeletor
Get the sizes of the proposed deletions
getSizes.DiscreteInsertor
Get the sizes of the proposed insertions
getState.Site
Get the current state of a Site object
getStates.Sequence
Get the states of a set of Site objects aggregated by a...
getString.Sequence
Get the string representation of a Sequence object
getSymbolFreqs.Sequence
Get a table with the frequencies of the states of a...
getSymbolLength.Alphabet
Get the length of the symbols in a given alphabet object
getSymbols.Alphabet
Get the symbol set from an Alphabet object
getTableId.CodonAlphabet
Get the genetic code id
getTemplateSeq.GeneralInsertor
Get the template sequence object
getTheta.T92
Get the GC content
getTipLabels.PhyloSim
Get the tip labels from a phylo object aggregated by a...
getTips.PhyloSim
Get the node identifiers of the tip nodes from a PhyloSim...
getToleranceMargin.FastFieldDeletor
Get the tolerance margin
getTotalRatesFromRange.Sequence
Get the vector of total site rates for a collection of Site...
getTotalRate.Site
Get the total active event rate
getTotalRates.Sequence
Get the total site rates from a Sequence object
getTransTable.CodonAlphabet
Get the list storing the genetic code table
getTreeLength.PhyloSim
Get the tree length from a PhyloSim object
getType.Alphabet
Get Alphabet obejct type
getType.BrownianInsertor
Get the type of the BrownianInsertor process
getType.FastFieldDeletor
Get the type of a FastFieldDeletor object
getUniqueAlphabets.Sequence
Get the list of unique Alphabet objects associated to Site...
getUniqueProcesses.Sequence
Get the list of unique Process instances attached to the Site...
getWriteProtected.Alphabet
Check if the object is write protected
getWriteProtected.Event
Check if the object is write protected
getWriteProtected.Process
Check if the object is write protected
getWriteProtected.QMatrix
Check if the object is write protected
getWriteProtected.Sequence
Check if the object is write protected
globalConsistencyCheck.PSRoot
Check the consistency of all objects inheriting form PSRoot...
GTR
The GTR class
GY94
The GY94 class
hasSiteSpecificParameter.Process
Check if a Process object has the site-process specific...
hasSymbols.Alphabet
Check if an Alphabet object has a given set of symbols
hasUndefinedRate.GeneralInDel
Check whether the general rate of a GeneralInDel object is...
hasUndefinedRate.GeneralSubstitution
Check if a GeneralSubstitution object has undefined rates
hasUndefinedRate.Process
Check if the Process object has undefined rate parameters
hasUndefinedRate.ToleranceSubstitution
Check if a ToleranceSubstitution object has undefined rates
HKY
The HKY class
insertSequence.Sequence
Insert a Sequence object into another Sequence object after a...
intersect.list.PSRoot
Utility method returning the intersection of two lists
is.Alphabet
Check if an object is an instance of the Alphabet class
isAttached.Site
Check whether a Process object is attached to a Site object
is.CodonAlphabet
Check if an object inherits from CodonAlphabet
is.CodonUNREST
Check whether an object inherits from CodonUNREST
isEmpty.Alphabet
Check if the symbol set is empty
is.Event
Check whether an object inherits from the class Event
is.GeneralDeletor
Check whether an object inherits from GeneralDeletor
is.GeneralInDel
Check if an object inherits from the GeneralInDel class
is.GeneralInsertor
Check whether an object inherits from GeneralInsertor
is.GeneralSubstitution
Check if an object is an instance of the GeneralSubstitution...
is.GY94
Check whether an object inherits from GY94
is.na.PSRoot
Check if a PSRoot object is NA
is.phylo
Check if an object is an instance of the phylo class
is.Process
Check if an object is an instance of the Process class
is.PSRoot
Check if an object inherits from PSRoot
is.QMatrix
Check if an object is an instance of the QMatrix class
is.Sequence
Check whether an object inherits from the Sequence class
is.Site
Check if an object is an instance of the Site class
isStartCodon.CodonAlphabet
Check if a codon is a start codon
isStopCodon.CodonAlphabet
Check if a codon is a stop codon
is.tip.PhyloSim
Check if a node is a tip
is.ToleranceSubstitution
Check if an object is an instance of the...
JC69
The JC69 class
JTT
The JTT empirical amino acid substitution model
JTT.dcmut
The JTT.dcmut empirical amino acid substitution model
K80
The K80 class
K81
The K81 class
LG
The LG empirical amino acid substitution model
ll.PSRoot
Display detailed information about the virtual fields and...
Log.PhyloSim
Save a message in the PhyloSim log file
mtArt
The mtArt empirical amino acid substitution model
mtMam
The mtMam empirical amino acid substitution model
mtREV24
The mtREV24 empirical amino acid substitution model
MtZoa
The MtZoa empirical amino acid substitution model
my.all.equal.PSRoot
Test if two objects are nearly equal
newAAMatrix.AminoAcidSubst
Undocumented method
newMatrix.CodonSubst
New codon substitution matrix from PAML file
NucleotideAlphabet
The NucleotideAlphabet class
NucleotideSequence
The NucleotideSequence class
omegaHist.CodonSequence
Plot a histogram of omega values from a range
omegaVarM0.CodonSequence
The M0 (one-ratio) model of variable omega ratios among sites
omegaVarM1.CodonSequence
The M1 (neutral) model of variable omega ratios among sites
omegaVarM2.CodonSequence
The M2 (selection) model of variable omega ratios among sites
omegaVarM3.CodonSequence
The M3 (discrete) model of variable omega ratios among sites
omegaVarM4.CodonSequence
The M4 (freqs) model of variable omega ratios among sites
PAM
The PAM empirical amino acid substitution model
PAM.dcmut
The PAM.dcmut empirical amino acid substitution model
Perform.Event
Perform an event
PhyloSim
The PhyloSim class
plot.ContinuousDeletor
Plot the density of proposed lengths
plot.ContinuousInsertor
Plot the density of proposed lengths
plot.DiscreteDeletor
Plot the deletion length distribution
plot.DiscreteInsertor
Plot the insertion length distribution
plot.GeneralSubstitution
Create a bubble plot of the substitution process
plotParametersAtSites.Sequence
Plot the value of a site-process specifc paramter for a...
plot.PhyloSim
Plot a PhyloSim object
plot.Sequence
Plot the total site rates for a collection of Site objects...
plot.ToleranceSubstitution
Create a bubble plot of the substitution process
plusGamma.Sequence
Sample the rate multiplier parameters of a Process from a...
plusInvGamma.Sequence
Sample the rate multiplier parameters of a Process from an...
print.PSRootSummary
Print out a PSRootSummary object
print.QMatrix
Print the character representation of a QMatrix object
Process
The Process class
proposeLength.GeneralInDel
Propose indel length
PSRoot
The root class for all phylosim objects
PSRootSummary
The PSRootSummary class
QMatrix
The QMatrix class
readAlignment.PhyloSim
Read alignment from file
readTree.PhyloSim
Read tree from file
rescaleQMatrix.GeneralSubstitution
Rescale the scaled rate matrix of a QMatrix object aggregated...
rescaleQMatrix.ToleranceSubstitution
Rescale the scaled rate matrix of a QMatrix object aggregated...
revComp.NucleotideSequence
Reverse complmenet a NucleotideSequence object
sampleState.GeneralSubstitution
Sample a state from the equlibrium distribution of a...
sampleStates.Sequence
Sample the states for a collection of Site objects aggregated...
sampleState.ToleranceSubstitution
Sample a state from the equlibrium distribution of a...
saveAlignment.PhyloSim
Save the alignment stored in a PhyloSim object in a Fasta...
Scale.QMatrix
Scale the scaled rate matrix stored in a QMatrix object by...
scaleTree.PhyloSim
Scale the branch lengths of a phylo object aggragted by a...
Sequence
The Sequence class
setAcceptBy.GeneralInDel
Set the function used for accepting/rejecting indel events
setAcceptWin.GeneralInsertor
Set the size of the acceptance window
setAlignment.PhyloSim
Forbidden action: setting the alignment stored in a PhyloSim...
setAlphabet.GeneralSubstitution
Set the Alphabet object aggregated by a GeneralSubstitution...
setAlphabet.Process
Assotiate an Alphabet object with a Process object
setAlphabet.QMatrix
Set the Alphabet object for a QMatrix object
setAlphabet.Site
Attach an Alphabet object to a Site object
setAlphabets.Sequence
Assotiate Alphabet objects to a set of Site objects...
setAlphabet.ToleranceSubstitution
Set the Alphabet object aggregated by a ToleranceSubstitution...
setAncestral.Sequence
Set the ancestral object of a Sequence object
setAncestral.Site
Forbidden action: setting the ancestral object for a Site...
setBaseFreqs.F81
Set the base frequency parameters
setBaseFreqs.F84
Set the base frequency parameters
setBaseFreqs.GTR
Set the base frequency parameters
setBaseFreqs.HKY
Set the base frequency parameters
setBaseFreqs.K80
Forbidden action: setting the base frequency parameters for a...
setBaseFreqs.K81
Forbidden action: setting the base frequency parameters for a...
setBaseFreqs.TN93
Set the base frequency parameters
setBigRate.Sequence
Forbidden action: setting the sum of total active event rates...
setBranchEvents.PhyloSim
Forbidden action: setting the list of events having...
setCodonFreqs.GY94
Get codon frequencies
setComments.PSRoot
Set the comments associated with an object
setCumulativeRates.Sequence
Forbidden action: setting the cumulative rates for the sites...
setDeletionTolerance.Sequence
Set the deletion tolerance site-process specific parameter...
setDist.ContinuousDeletor
Set the length sampling expression
setDist.ContinuousInsertor
Set the length sampling expression
setEdges.PhyloSim
Forbidden action: setting the edge matrix for a phylo object...
setEquDist.GeneralSubstitution
Set the equilibrium distribution for a GeneralSubstitution...
setEquDist.ToleranceSubstitution
Set the equilibrium distribution for a ToleranceSubstitution...
setEvents.Site
Forbidden action: setting the list of active events for a...
setGenerateBy.GeneralInsertor
Set the function object used for generating inserts
setHandler.Event
Forbidden action: setting the handler function of an Event...
setId.PhyloSim
Forbidden action: setting the unique identifier of a PhyloSim...
setId.Process
Forbidden action: setting the unique Process object...
setId.QMatrix
Forbidden action: setting the unique identifier for a QMatrix...
setId.Sequence
Forbidden action: setting the unique identifier of a Sequence...
setInsertHook.GeneralInsertor
Set the insert hook function
setInsertionTolerance.Sequence
Set the insertion tolerance site-process specific parameter...
setKappa.F84
Get the transition transversion rate ratio
setKappa.GY94
Set the transition/transversion rate ratio
setLengthParam1.FastFieldDeletor
Set the first length parameter
setLengthParam2.FastFieldDeletor
Set the second length parameter
setLength.Sequence
Forbidden action: setting the length of a Sequence object
setLogFile.PhyloSim
Set the name of the file used for logging
setLogLevel.PhyloSim
Set the log level for a given PhyloSim object
setMatrix.QMatrix
Forbidden action: setting the unscaled rate matrix for a...
setMaxLength.ContinuousDeletor
Set the maximum length
setMaxLength.ContinuousInsertor
Set the maximum length
setMethodsList.PSRoot
Forbidden action: setting the list of applicable methods for...
setName.Event
Set the name of an Event object
setName.PhyloSim
Set the name of a PhyloSim object
setName.Process
Set the name of a Process object
setName.QMatrix
Set the name of a QMatrix object
setName.Sequence
Set the name of a Sequence object
setNedges.PhyloSim
Forbidden action: setting the number of edges for phylo...
setNodes.PhyloSim
Forbidden action: setting the node identifiers for a PhyloSim...
setNtips.PhyloSim
Forbidden action: setting the number of the tips for a phylo...
setOmegas.CodonSequence
Set the omegas for a collection of sites
setParameterAtSite.Process
Set the value of a site-process specific paramter in a Site...
setParameterAtSites.Sequence
Set the values of a site-process specific paramater for a...
setPhylo.PhyloSim
Set the phylo object for a PhyloSim object
setPosition.Event
Set the position of the Site object associated to an Event...
setProbs.DiscreteDeletor
Set the deletion length probabilities
setProbs.DiscreteInsertor
Set the insertion length probabilities
setProcesses.Sequence
Specify a set of Process objects to be attached to a set of...
setProcesses.Site
Specify the list of Process objects attached to a Site object
setProcess.Event
Set the generator process for an Event object
setProcess.QMatrix
Assotiate a process object with a QMatrix object
setProposeBy.GeneralInDel
Set the function used for proposing indel lengths
setQMatrix.GeneralSubstitution
Set the QMatrix object aggregated by a GeneralSubstitution...
setQMatrix.ToleranceSubstitution
Set the QMatrix object aggregated by a ToleranceSubstitution...
setRate.Event
Set the rate of an Event object
setRate.GeneralInDel
Set the general rate
setRate.GeneralSubstitution
Set an unscaled rate for an event from a GeneralSubstitution...
setRate.GY94
Set an unscaled rate for an event from a GY94 object
setRateList.GeneralSubstitution
Setting the rates for a GeneralSubstitution object
setRateList.QMatrix
Setting the unscaled rates stored in a QMatrix object
setRateList.ToleranceSubstitution
Setting the rates for a ToleranceSubstitution object
setRateMultipliers.Sequence
Set the values of the rate multiplier parameters for a given...
setRateParam.F81
Forbidden action: getting the list of rate parameters
setRateParam.F84
Set the value of a rate parameter
setRateParam.GTR
Set the value of a rate parameter
setRateParam.HKY
Set the value of a rate parameter
setRateParam.K80
Set the value of a rate parameter
setRateParam.K81
Set the value of a rate parameter
setRateParamList.F81
Forbidden action: getting the list of rate parameters
setRateParamList.F84
Set the rate parameters
setRateParamList.GTR
Set the rate parameters
setRateParamList.HKY
Set the rate parameters
setRateParamList.K80
Set the rate parameters
setRateParamList.K81
Set the rate parameters
setRateParamList.T92
Set the rate parameters
setRateParamList.TN93
Set the rate parameters
setRateParam.T92
Set the value of a rate parameter
setRateParam.TN93
Set the value of a rate parameter
setRate.QMatrix
Set an unscaled rate in a QMatrix object
setRate.ToleranceSubstitution
Set an unscaled rate for an event from a...
setRootNode.PhyloSim
Forbidden action: setting the identifier of the root node for...
setRootSeq.PhyloSim
Set the root sequence for a PhyloSim object
setScale.BrownianInsertor
Set scale parameter
setScaledMatrix.QMatrix
Forbidden action: setting the scaled rate matrix for a...
setSequence.Site
Assotiate a Sequence object with a Site object
setSequences.PhyloSim
Forbidden action: setting the Sequence objects associated...
setSite.Event
Assotiate an Event object with a Site object
setSiteSpecificParamIds.Process
Forbidden action: setting the paramter identifiers of the...
setSiteSpecificParamList.Process
Forbidden action: setting the site specific paramter list for...
setSize.Alphabet
Forbidden action: setting the symbol set size of an Alphabet...
setSizes.DiscreteDeletor
Set the sizes of the proposed deletions
setSizes.DiscreteInsertor
Set the sizes of the proposed insertions
setState.Site
Set the state of a Site object
setStates.Sequence
Set the states for a set of Site objects aggregated by a...
setString.Sequence
Forbidden action: setting the string representation of a...
setSymbolLength.Alphabet
Forbidden action: setting the symbol length for an Alphabet...
setSymbols.Alphabet
Specify a new symbol set for an Alphabet object
setTableId.CodonAlphabet
Forbidden action: setting the genetic code id
setTemplateSeq.GeneralInsertor
Set the template sequence object
setTheta.T92
Set the GC content
setTipLabels.PhyloSim
Forbidden action: setting the tip labels for a phylo object...
setTips.PhyloSim
Forbidden action: setting the node identifiers of the tip...
setToleranceMargin.FastFieldDeletor
Set the tolerance margin
setTotalRate.Site
Forbidden action: setting the total active event rate for a...
setTotalRates.Sequence
Forbidden action: setting the list of total site rates for a...
setTransTable.CodonAlphabet
Forbidden action: setting the genetic code table for a...
setTreeLength.PhyloSim
Forbidden action: setting the tree length for a PhyloSim...
setType.Alphabet
Set Alphabet object type
setType.BrownianInsertor
Forbidden action: setting the type of a BrownianInsertor...
setType.FastFieldDeletor
Forbidden action: setting the type of a FastFieldDeletor...
setUniqueAlphabets.Sequence
Forbidden action: setting the list of unique Alphabet objects...
setUniqueProcesses.Sequence
Forbidden action: setting the list of unique Process...
setWriteProtected.Alphabet
Set the write protection field for an object
setWriteProtected.Event
Set the write protection field for an object
setWriteProtected.Process
Set the write protection field for an object
setWriteProtected.QMatrix
Set the write protection field for a QMatrix object
setWriteProtected.Sequence
Set the write protection field for an object
Simulate.PhyloSim
Run a simulation according to a PhyloSim object
Site
The Site class
stringLength
Returns the string length of the character representation of...
stringLengthVector
Returns the string lengths of the character represenations of...
summary.Alphabet
Summarize the properties of an object
summary.AminoAcidSubst
Summarize the properties of an object
summary.BinarySubst
Summarize the properties of an object
summary.BrownianInsertor
Summarize the properties of an object
summary.CodonAlphabet
Summarize the properties of an object
summary.CodonSubst
Summarize the properties of an object
summary.ContinuousDeletor
Summarize the properties of an object
summary.ContinuousInsertor
Summarize the properties of an object
summary.DiscreteDeletor
Summarize the properties of an object
summary.DiscreteInsertor
Summarize the properties of an object
summary.Event
Summarize the properties of an object
summary.F81
Summarize the properties of an object
summary.F84
Summarize the properties of an object
summary.FastFieldDeletor
Summarize the properties of an object
summary.GeneralDeletor
Summarize the properties of an object
summary.GeneralInDel
Summarize the properties of an object
summary.GeneralInsertor
Summarize the properties of an object
summary.GeneralSubstitution
Summarize the properties of an object
summary.GTR
Summarize the properties of an object
summary.GY94
Summarize the properties of an object
summary.HKY
Summarize the properties of an object
summary.JC69
Summarize the properties of an object
summary.K80
Summarize the properties of an object
summary.K81
Summarize the properties of an object
summary.PhyloSim
Summarize the properties of an object
summary.Process
Summarize the properties of an object
summary.PSRoot
Summarize the properties of an object
summary.QMatrix
Summarize the properties of an object
summary.Sequence
Summarize the properties of an object
summary.Site
Summarize the properties of an object
summary.T92
Summarize the properties of an object
summary.TN93
Summarize the properties of an object
summary.ToleranceSubstitution
Summarize the properties of an object
summary.UNREST
Summarize the properties of an object
T92
The T92 class
TN93
The TN93 class
ToleranceSubstitution
The ToleranceSubstitution class
translateCodon.CodonAlphabet
Translate a codon
Translate.CodonSequence
Translate a CodonSequence object
Undocumented.PhyloSim
Undocumented object (PhyloSim package)
UNREST
The UNREST class
virtualAssignmentForbidden.PSRoot
Throws an error message informing the user about forbidden...
WAG
The WAG empirical amino acid substitution model

Files in this package

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