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