Files in phylosim
Flexible Simulations of Biological Sequence Evolution

inst
inst/extdata
inst/extdata/MtZoa.dat
inst/extdata/wag.dat
inst/extdata/g1974a.dat
inst/extdata/miyata.dat
inst/extdata/ECMunrest.dat
inst/extdata/mtArt.dat
inst/extdata/jones.dat
inst/extdata/dayhoff.dat
inst/extdata/mtREV24.dat
inst/extdata/g1974c.dat
inst/extdata/ECMrest.dat
inst/extdata/g1974p.dat
inst/extdata/cpREV.dat
inst/extdata/g1974v.dat
inst/extdata/mtmam.dat
inst/extdata/lg.dat
inst/extdata/dayhoff-dcmut.dat
inst/extdata/grantham.dat
inst/extdata/jones-dcmut.dat
inst/doc
inst/doc/PhyloSim.pdf
inst/doc/PhyloSim.Rnw
inst/doc/PhyloSim.R
NAMESPACE
data
data/WAG.RData
data/mtArt.RData
data/JTT.dcmut.RData
data/ECMrest.RData
data/LG.RData
data/PAM.dcmut.RData
data/JTT.RData
data/mtREV24.RData
data/ECMunrest.RData
data/MtZoa.RData
data/cpREV.RData
data/mtMam.RData
data/PAM.RData
R
R/GeneralSubstitution.R R/CodonSubst.R R/DiscreteDeletor.R R/DiscreteInsertor.R R/ContinuousInsertor.R R/FieldDeletor.R R/BinarySubst.R R/PopularAlphabets.R R/GeneralInDel.R R/Alphabet.R R/Event.R R/AminoAcidSubst.R R/QMatrix.R R/PSRoot.R R/CodonAlphabet.R R/Site.R R/BrownianInsertor.R R/PopularSequences.R R/AminoAcidMatrices.R R/CodonModels.R R/NucleotideModels.R R/Sequence.R R/EmpiricalCodonMatrices.R R/ContinuousDeletor.R R/PhyloSimSource.R R/PhyloSim.R R/Process.R R/ToleranceSubstitution.R
vignettes
vignettes/Makefile
vignettes/PhyloSim.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/hasUndefinedRate.GeneralInDel.Rd man/summary.F84.Rd man/omegaVarM0.CodonSequence.Rd man/setBaseFreqs.GTR.Rd man/setRateParam.F84.Rd man/checkConsistency.K81.Rd man/checkConsistency.Sequence.Rd man/getName.Event.Rd man/print.QMatrix.Rd man/setRate.QMatrix.Rd man/getTemplateSeq.GeneralInsertor.Rd man/setTransTable.CodonAlphabet.Rd man/BrownianInsertor.Rd man/setAlphabet.Site.Rd man/is.GeneralDeletor.Rd man/buildFromPAML.AminoAcidSubst.Rd man/summary.PSRoot.Rd man/ContinuousInsertor.Rd man/checkConsistency.BinarySubst.Rd man/setAlphabet.ToleranceSubstitution.Rd man/checkConsistency.ToleranceSubstitution.Rd man/setRateParamList.GTR.Rd man/summary.GTR.Rd man/setProposeBy.GeneralInDel.Rd man/insertSequence.Sequence.Rd man/getHandler.Event.Rd man/setRateList.ToleranceSubstitution.Rd man/as.character.Process.Rd man/setLengthParam2.FastFieldDeletor.Rd man/BinarySubst.Rd man/checkConsistency.ContinuousInsertor.Rd man/getEventRateAtSite.GeneralSubstitution.Rd man/summary.GeneralInsertor.Rd man/checkConsistency.GeneralDeletor.Rd man/setName.QMatrix.Rd man/setRateList.GeneralSubstitution.Rd man/setBaseFreqs.F84.Rd man/getProposeBy.GeneralInDel.Rd man/setName.Process.Rd man/getInsertHook.GeneralInsertor.Rd man/getOmegas.CodonSequence.Rd man/getEquDist.GeneralSubstitution.Rd man/newAAMatrix.AminoAcidSubst.Rd man/hasUndefinedRate.Process.Rd man/getType.FastFieldDeletor.Rd man/setAcceptBy.GeneralInDel.Rd man/getCumulativeRatesFromRange.Sequence.Rd man/UNREST.Rd man/is.tip.PhyloSim.Rd man/setRate.GY94.Rd man/getBranchEvents.PhyloSim.Rd man/setAlignment.PhyloSim.Rd man/getComments.PSRoot.Rd man/setRate.GeneralInDel.Rd man/CodonAlphabet.Rd man/is.CodonUNREST.Rd man/setMaxLength.ContinuousDeletor.Rd man/cpREV.Rd man/checkConsistency.GeneralInDel.Rd man/clone.Process.Rd man/setNtips.PhyloSim.Rd man/checkConsistency.CodonSequence.Rd man/setLength.Sequence.Rd man/checkConsistency.BrownianInsertor.Rd man/getType.BrownianInsertor.Rd man/setWriteProtected.Process.Rd man/setRateParam.HKY.Rd man/getRateParamList.HKY.Rd man/getBaseFreqs.TN93.Rd man/JC69.Rd man/getMaxLength.ContinuousInsertor.Rd man/deleteSubSequence.Sequence.Rd man/hasUndefinedRate.ToleranceSubstitution.Rd man/flagTotalRate.Site.Rd man/is.Event.Rd man/checkConsistency.AminoAcidSubst.Rd man/HKY.Rd man/getEquDist.ToleranceSubstitution.Rd man/getProcesses.Sequence.Rd man/getDist.ContinuousDeletor.Rd man/setType.BrownianInsertor.Rd man/getAlphabet.QMatrix.Rd man/BrownianPath.BrownianInsertor.Rd man/ECMunrest.Rd man/PhyloSim.Rd man/setRootSeq.PhyloSim.Rd man/checkConsistency.K80.Rd man/getRate.GeneralInDel.Rd man/PSRootSummary.Rd man/getEvents.Sequence.Rd man/checkConsistency.GY94.Rd man/getRateList.GeneralSubstitution.Rd man/getWriteProtected.Sequence.Rd man/getSiteSpecificParamIds.Process.Rd man/print.PSRootSummary.Rd man/checkConsistency.DiscreteInsertor.Rd man/setTips.PhyloSim.Rd man/hasSiteSpecificParameter.Process.Rd man/summary.CodonSubst.Rd man/setBranchEvents.PhyloSim.Rd man/getName.Process.Rd man/setRateParam.T92.Rd man/getTransTable.CodonAlphabet.Rd man/detachSeqFromNode.PhyloSim.Rd man/setType.Alphabet.Rd man/checkConsistency.ContinuousDeletor.Rd man/enableVirtual.PSRoot.Rd man/checkConsistency.GTR.Rd man/setDeletionTolerance.Sequence.Rd man/setRateMultipliers.Sequence.Rd man/setRateParam.K81.Rd man/getParameterAtSite.Process.Rd man/getRate.Event.Rd man/setEdges.PhyloSim.Rd man/getName.Sequence.Rd man/setTemplateSeq.GeneralInsertor.Rd man/setDist.ContinuousDeletor.Rd man/plotParametersAtSites.Sequence.Rd man/Perform.Event.Rd man/getEdges.PhyloSim.Rd man/getScale.BrownianInsertor.Rd man/summary.Sequence.Rd man/setParameterAtSite.Process.Rd man/setWriteProtected.QMatrix.Rd man/stringLength.Rd man/clone.GeneralSubstitution.Rd man/setRateParam.F81.Rd man/summary.ContinuousDeletor.Rd man/getSymbolFreqs.Sequence.Rd man/getEventsAtSite.GeneralDeletor.Rd man/setProbs.DiscreteInsertor.Rd man/getDeletionTolerance.Sequence.Rd man/getTipLabels.PhyloSim.Rd man/summary.DiscreteDeletor.Rd man/getAlphabet.Site.Rd man/as.character.Alphabet.Rd man/proposeLength.GeneralInDel.Rd man/getGenerateBy.GeneralInsertor.Rd man/QMatrix.Rd man/buildFromPAML.CodonSubst.Rd man/getAcceptBy.GeneralInDel.Rd man/attachProcess.Site.Rd man/getOmegaScalingFactor.GY94.Rd man/getKappa.GY94.Rd man/is.GeneralInsertor.Rd man/getLogFile.PhyloSim.Rd man/setAlphabet.Process.Rd man/setRateParamList.K80.Rd man/setType.FastFieldDeletor.Rd man/setAlphabet.QMatrix.Rd man/checkConsistency.T92.Rd man/getToleranceMargin.FastFieldDeletor.Rd man/summary.GeneralSubstitution.Rd man/rescaleQMatrix.ToleranceSubstitution.Rd man/Log.PhyloSim.Rd man/setAncestral.Site.Rd man/getRateList.QMatrix.Rd man/as.character.ToleranceSubstitution.Rd man/getEventsAtSite.ToleranceSubstitution.Rd man/getKappa.F84.Rd man/setPosition.Event.Rd man/getSymbolLength.Alphabet.Rd man/getAncestral.Sequence.Rd man/getMatrix.QMatrix.Rd man/setRateList.QMatrix.Rd man/is.GeneralInDel.Rd man/getEdge.PhyloSim.Rd man/attachHookToNode.PhyloSim.Rd man/summary.F81.Rd man/summary.BrownianInsertor.Rd man/setRateParamList.K81.Rd man/as.character.QMatrix.Rd man/hasSymbols.Alphabet.Rd man/setAlphabet.GeneralSubstitution.Rd man/setScaledMatrix.QMatrix.Rd man/omegaVarM2.CodonSequence.Rd man/getEventRateAtSite.ToleranceSubstitution.Rd man/summary.DiscreteInsertor.Rd man/setBaseFreqs.K81.Rd man/summary.HKY.Rd man/getRateParamList.TN93.Rd man/getWriteProtected.QMatrix.Rd man/setHandler.Event.Rd man/as.character.Event.Rd man/MtZoa.Rd man/sampleState.ToleranceSubstitution.Rd man/getRateParamList.GTR.Rd man/getProcesses.Site.Rd man/getRateParam.F81.Rd man/setRate.GeneralSubstitution.Rd man/GY94.Rd man/attachSeqToNode.PhyloSim.Rd man/setKappa.F84.Rd man/omegaVarM3.CodonSequence.Rd man/getRateParamList.T92.Rd man/is.GeneralSubstitution.Rd man/getRateParam.GTR.Rd man/summary.PhyloSim.Rd man/checkConsistency.FastFieldDeletor.Rd man/getTreeLength.PhyloSim.Rd man/getNtips.PhyloSim.Rd man/getCumulativeRates.Sequence.Rd man/getProbs.DiscreteInsertor.Rd man/setId.PhyloSim.Rd man/plot.DiscreteInsertor.Rd man/getWriteProtected.Alphabet.Rd man/setGenerateBy.GeneralInsertor.Rd man/setEquDist.ToleranceSubstitution.Rd man/checkConsistency.Event.Rd man/virtualAssignmentForbidden.PSRoot.Rd man/getBaseFreqs.GTR.Rd man/Scale.QMatrix.Rd man/Sequence.Rd man/setTableId.CodonAlphabet.Rd man/setSizes.DiscreteDeletor.Rd man/getTips.PhyloSim.Rd man/checkConsistency.HKY.Rd man/as.character.GeneralSubstitution.Rd man/Event.Rd man/AnyAlphabet.Rd man/FastFieldDeletor.Rd man/getEventsAtSite.Process.Rd man/checkConsistency.F84.Rd man/isAttached.Site.Rd man/GeneralSubstitution.Rd man/Alphabet.Rd man/Debug.PhyloSim.Rd man/PAM.dcmut.Rd man/getRateParam.T92.Rd man/GeneralDeletor.Rd man/ll.PSRoot.Rd man/getTotalRatesFromRange.Sequence.Rd man/getParameterAtSites.Sequence.Rd man/hasUndefinedRate.GeneralSubstitution.Rd man/setKappa.GY94.Rd man/ContinuousDeletor.Rd man/plusInvGamma.Sequence.Rd man/Site.Rd man/is.Process.Rd man/setMethodsList.PSRoot.Rd man/getAlphabet.GeneralSubstitution.Rd man/plot.PhyloSim.Rd man/readTree.PhyloSim.Rd man/checkConsistency.GeneralInsertor.Rd man/plot.Sequence.Rd man/getPhylo.PhyloSim.Rd man/getProcess.QMatrix.Rd man/setWriteProtected.Alphabet.Rd man/summary.Process.Rd man/getLengthParam2.FastFieldDeletor.Rd man/checkConsistency.QMatrix.Rd man/getBaseFreqs.F81.Rd man/getString.Sequence.Rd man/Undocumented.PhyloSim.Rd man/setSiteSpecificParamIds.Process.Rd man/getEventRate.GeneralSubstitution.Rd man/summary.ContinuousInsertor.Rd man/setId.Sequence.Rd man/Translate.CodonSequence.Rd man/getSites.Sequence.Rd man/checkConsistency.DiscreteDeletor.Rd man/as.character.Sequence.Rd man/detachHookFromNode.PhyloSim.Rd man/getAlignment.PhyloSim.Rd man/getTableId.CodonAlphabet.Rd man/F84.Rd man/my.all.equal.PSRoot.Rd man/checkConsistency.CodonAlphabet.Rd man/getRateParam.HKY.Rd man/summary.FastFieldDeletor.Rd man/getEventsAtSite.GeneralInsertor.Rd man/CodonSequence.Rd man/getName.PhyloSim.Rd man/getRateParam.K81.Rd man/BinaryAlphabet.Rd man/getRateList.ToleranceSubstitution.Rd man/omegaVarM1.CodonSequence.Rd man/getEvents.Site.Rd man/checkConsistency.Process.Rd man/checkConsistency.Alphabet.Rd man/mtArt.Rd man/summary.ToleranceSubstitution.Rd man/setName.Event.Rd man/is.ToleranceSubstitution.Rd man/checkConsistency.GeneralSubstitution.Rd man/getPosition.Event.Rd man/WAG.Rd man/setQMatrix.GeneralSubstitution.Rd man/setSize.Alphabet.Rd man/NucleotideAlphabet.Rd man/getBaseFreqs.K81.Rd man/setPhylo.PhyloSim.Rd man/summary.UNREST.Rd man/as.character.PhyloSim.Rd man/setRateParamList.F84.Rd man/getEventRate.QMatrix.Rd man/stringLengthVector.Rd man/getRateParamList.K81.Rd man/getSizes.DiscreteInsertor.Rd man/setRate.ToleranceSubstitution.Rd man/getWriteProtected.Event.Rd man/summary.CodonAlphabet.Rd man/setTotalRate.Site.Rd man/GeneralInsertor.Rd man/setName.Sequence.Rd man/rescaleQMatrix.GeneralSubstitution.Rd man/plot.ContinuousInsertor.Rd man/setLogFile.PhyloSim.Rd man/summary.K80.Rd man/readAlignment.PhyloSim.Rd man/summary.GY94.Rd man/setMaxLength.ContinuousInsertor.Rd man/as.character.Site.Rd man/getUniqueAlphabets.Sequence.Rd man/setSizes.DiscreteInsertor.Rd man/getAlphabet.Process.Rd man/setEquDist.GeneralSubstitution.Rd man/getBaseFreqs.HKY.Rd man/setCumulativeRates.Sequence.Rd man/is.GY94.Rd man/T92.Rd man/detachProcess.Site.Rd man/setQMatrix.ToleranceSubstitution.Rd man/setBaseFreqs.TN93.Rd man/setSequences.PhyloSim.Rd man/AminoAcidSequence.Rd man/intersect.list.PSRoot.Rd man/setSymbolLength.Alphabet.Rd man/getSize.Alphabet.Rd man/checkConsistency.PSRootSummary.Rd man/setUniqueProcesses.Sequence.Rd man/setCodonFreqs.GY94.Rd man/getAcceptWin.GeneralInsertor.Rd man/copySubSequence.Sequence.Rd man/getSeqFromNode.PhyloSim.Rd man/plot.ContinuousDeletor.Rd man/setOmegas.CodonSequence.Rd man/setAlphabets.Sequence.Rd man/areSynonymous.CodonAlphabet.Rd man/TN93.Rd man/setEvents.Site.Rd man/is.Site.Rd man/getLengthParam1.FastFieldDeletor.Rd man/setComments.PSRoot.Rd man/clone.Sequence.Rd man/summary.TN93.Rd man/getRateParamList.F84.Rd man/getProbs.DiscreteDeletor.Rd man/checkConsistency.PhyloSim.Rd man/setString.Sequence.Rd man/summary.K81.Rd man/generateInsert.GeneralInsertor.Rd man/getRateParamList.K80.Rd man/getId.QMatrix.Rd man/getSequence.Site.Rd man/summary.GeneralInDel.Rd man/NucleotideSequence.Rd man/setMatrix.QMatrix.Rd man/setTotalRates.Sequence.Rd man/checkConsistency.PSRoot.Rd man/omegaVarM4.CodonSequence.Rd man/checkConsistency.TN93.Rd man/getName.QMatrix.Rd man/getNedges.PhyloSim.Rd man/getAncestral.Site.Rd man/setRateParamList.F81.Rd man/setParameterAtSites.Sequence.Rd man/getSiteSpecificParamList.Process.Rd man/setRate.Event.Rd man/setStates.Sequence.Rd man/getRateParam.TN93.Rd man/getSite.Event.Rd man/000==.Process.Rd man/plot.GeneralSubstitution.Rd man/Simulate.PhyloSim.Rd man/getMethodsList.PSRoot.Rd man/summary.GeneralDeletor.Rd man/setLogLevel.PhyloSim.Rd man/clone.ToleranceSubstitution.Rd man/getRateParamList.F81.Rd man/isEmpty.Alphabet.Rd man/getId.PhyloSim.Rd man/setName.PhyloSim.Rd man/setLengthParam1.FastFieldDeletor.Rd man/getRate.ToleranceSubstitution.Rd man/setTipLabels.PhyloSim.Rd man/setAncestral.Sequence.Rd man/globalConsistencyCheck.PSRoot.Rd man/getRootNode.PhyloSim.Rd man/ToleranceSubstitution.Rd man/setProbs.DiscreteDeletor.Rd man/setWriteProtected.Event.Rd man/setRateParam.GTR.Rd man/PSRoot.Rd man/setBigRate.Sequence.Rd man/summary.Site.Rd man/AminoAcidAlphabet.Rd man/JTT.Rd man/checkConsistency.JC69.Rd man/isStartCodon.CodonAlphabet.Rd man/setTheta.T92.Rd man/checkConsistency.CodonUNREST.Rd man/is.Alphabet.Rd man/getRootSeq.PhyloSim.Rd man/ECMrest.Rd man/getTotalRates.Sequence.Rd man/getRateParam.K80.Rd man/sampleStates.Sequence.Rd man/CodonUNREST.Rd man/getTheta.T92.Rd man/getEventsAtSite.GeneralSubstitution.Rd man/getNodes.PhyloSim.Rd man/checkConsistency.CodonSubst.Rd man/getDist.ContinuousInsertor.Rd man/plot.DiscreteDeletor.Rd man/getId.Process.Rd man/is.phylo.Rd man/setId.Process.Rd man/setRateParamList.TN93.Rd man/is.PSRoot.Rd man/getProcess.Event.Rd man/setState.Site.Rd man/K81.Rd man/setInsertHook.GeneralInsertor.Rd man/setProcess.Event.Rd man/setBaseFreqs.F81.Rd man/is.Sequence.Rd man/getLength.Sequence.Rd man/getInsertionTolerance.Sequence.Rd man/getLogLevel.PhyloSim.Rd man/newMatrix.CodonSubst.Rd man/setRateParamList.T92.Rd man/F81.Rd man/sampleState.GeneralSubstitution.Rd man/setId.QMatrix.Rd man/getSequences.PhyloSim.Rd man/000==.Alphabet.Rd man/setRateParam.TN93.Rd man/scaleTree.PhyloSim.Rd man/getSizes.DiscreteDeletor.Rd man/plot.ToleranceSubstitution.Rd man/setRateParamList.HKY.Rd man/getId.Sequence.Rd man/exportStatTree.PhyloSim.Rd man/DiscreteInsertor.Rd man/AminoAcidSubst.Rd man/summary.AminoAcidSubst.Rd man/summary.JC69.Rd man/omegaHist.CodonSequence.Rd man/setDist.ContinuousInsertor.Rd man/getMaxLength.ContinuousDeletor.Rd man/setSite.Event.Rd man/setProcesses.Site.Rd man/getRate.QMatrix.Rd man/setSymbols.Alphabet.Rd man/getEventsAtSite.GY94.Rd man/setScale.BrownianInsertor.Rd man/GTR.Rd man/getSymbols.Alphabet.Rd man/getCodonFreqs.GY94.Rd man/is.na.PSRoot.Rd man/summary.QMatrix.Rd man/setWriteProtected.Sequence.Rd man/setInsertionTolerance.Sequence.Rd man/getRate.GeneralSubstitution.Rd man/setNedges.PhyloSim.Rd man/PAM.Rd man/getEventRate.ToleranceSubstitution.Rd man/summary.T92.Rd man/translateCodon.CodonAlphabet.Rd man/setUniqueAlphabets.Sequence.Rd man/getRateParam.F84.Rd man/getScaledMatrix.QMatrix.Rd man/setBaseFreqs.HKY.Rd man/attachProcess.Sequence.Rd man/checkConsistency.Site.Rd man/getAlphabet.ToleranceSubstitution.Rd man/getQMatrix.GeneralSubstitution.Rd man/getType.Alphabet.Rd man/revComp.NucleotideSequence.Rd man/setSequence.Site.Rd man/GeneralInDel.Rd man/getTotalRate.Site.Rd man/getAlphabets.Sequence.Rd man/getRateMultipliers.Sequence.Rd man/getEventsAtSite.FastFieldDeletor.Rd man/saveAlignment.PhyloSim.Rd man/getBaseFreqs.K80.Rd man/LG.Rd man/is.QMatrix.Rd man/setProcesses.Sequence.Rd man/mtREV24.Rd man/JTT.dcmut.Rd man/checkConsistency.UNREST.Rd man/getQMatrix.ToleranceSubstitution.Rd man/summary.BinarySubst.Rd man/isStopCodon.CodonAlphabet.Rd man/setTreeLength.PhyloSim.Rd man/getBigRate.Sequence.Rd man/getBaseFreqs.F84.Rd man/is.CodonAlphabet.Rd man/setAcceptWin.GeneralInsertor.Rd man/checkConsistency.F81.Rd man/getState.Site.Rd man/summary.Alphabet.Rd man/setProcess.QMatrix.Rd man/setRateParam.K80.Rd man/DiscreteDeletor.Rd man/setToleranceMargin.FastFieldDeletor.Rd man/plusGamma.Sequence.Rd man/getAlignmentLength.PhyloSim.Rd man/setRootNode.PhyloSim.Rd man/K80.Rd man/setSiteSpecificParamList.Process.Rd man/CodonSubst.Rd man/summary.Event.Rd man/getUniqueProcesses.Sequence.Rd man/getStates.Sequence.Rd man/setBaseFreqs.K80.Rd man/mtMam.Rd man/BinarySequence.Rd man/clearStates.Sequence.Rd man/getWriteProtected.Process.Rd man/detachProcess.Sequence.Rd man/setNodes.PhyloSim.Rd man/Process.Rd
.Rinstignore
phylosim documentation built on May 29, 2017, 3:21 p.m.