├── .gitignore ├── Alphabet.R ├── AminoAcidMatrices.R ├── AminoAcidSubst.R ├── BinarySubst.R ├── BrownianInsertor.R ├── COPYING ├── COPYLEFT ├── CodonAlphabet.R ├── CodonModels.R ├── CodonSubst.R ├── ContinuousDeletor.R ├── ContinuousInsertor.R ├── DiscreteDeletor.R ├── DiscreteInsertor.R ├── EmpiricalCodonMatrices.R ├── Event.R ├── FieldDeletor.R ├── GeneralInDel.R ├── GeneralSubstitution.R ├── Makefile ├── NucleotideModels.R ├── PAMLdat ├── ECMrest.dat ├── ECMunrest.dat ├── MtZoa.dat ├── cpREV.dat ├── dayhoff-dcmut.dat ├── dayhoff.dat ├── g1974a.dat ├── g1974c.dat ├── g1974p.dat ├── g1974v.dat ├── grantham.dat ├── jones-dcmut.dat ├── jones.dat ├── lg.dat ├── miyata.dat ├── mtArt.dat ├── mtREV24.dat ├── mtmam.dat └── wag.dat ├── PSRoot.R ├── PhyloSim.R ├── PopularAlphabets.R ├── PopularSequences.R ├── Process.R ├── QMatrix.R ├── RData ├── .gitignore ├── ECMrest.RData ├── ECMunrest.RData ├── JTT.RData ├── JTT.dcmut.RData ├── LG.RData ├── MtZoa.RData ├── PAM.RData ├── PAM.dcmut.RData ├── WAG.RData ├── cpREV.RData ├── mtArt.RData ├── mtMam.RData └── mtREV24.RData ├── README.md ├── Sequence.R ├── Site.R ├── ToleranceSubstitution.R ├── cons_test ├── Makefile ├── README.md ├── aa_funcs.R ├── codon_funcs.R ├── common.R ├── constest_aa.R ├── constest_codon.R ├── constest_nucleotide.R ├── ctl │ ├── baseml.ctl │ ├── codeml_aa.ctl │ ├── codeml_codon.ctl │ └── wag.dat ├── nucleotide_funcs.R ├── results │ ├── .gitignore │ ├── constest_aa.log │ ├── constest_aa.pdf │ ├── constest_aa.tab │ ├── constest_codon.log │ ├── constest_codon.pdf │ ├── constest_codon.tab │ ├── constest_nucleotide.log │ ├── constest_nucleotide.pdf │ ├── constest_nucleotide.tab │ ├── times_aa.tab │ ├── times_codon.tab │ ├── times_nucleotide.tab │ ├── ttab_aa.tab │ ├── ttab_aa_r1.tex │ ├── ttab_codon.tab │ ├── ttab_codon_r1.tex │ ├── ttab_nucleotide.tab │ └── ttab_nucleotide_r1.tex ├── tree │ ├── test_tree.nwk │ └── test_tree.t ├── update_plots.R ├── update_ttabs.R └── utils.R ├── examples ├── .gitignore ├── data │ ├── 3taxa.nwk │ ├── 4taxa.nwk │ ├── PF02171_seed.fasta │ ├── PF02171_seed.nh │ ├── ensembl_genomic.fasta │ ├── ensembl_pax.fasta │ ├── ensembl_pax.nh │ ├── ensembl_pax_sub.fasta │ ├── ensembl_pax_sub.nh │ ├── mammals.nwk │ ├── slr_bigtree.fasta │ ├── slr_bigtree.nh │ ├── slrsim_bglobin_scores.fasta │ ├── slrsim_bglobin_scores.nh │ └── smalldemotree.nwk ├── example_3_clean.R ├── example_A1.R ├── example_V2.1.1.R ├── example_V2.1.2.R ├── example_V2.2.R ├── example_V2.3.R ├── example_V2.4.1-2.R ├── example_V2.4.3.R ├── example_V2.5.R ├── example_V2.6.R ├── example_V2.7.R ├── example_V3.1.R ├── example_V3.2.R ├── example_V3.3.R ├── example_V3.4.R ├── example_X1_plots.R ├── example_X2_tracks.R ├── example_X3_aln_length_tolerance.R ├── example_X4.R ├── example_X5.R ├── examples_class.R └── greg_scripts.R ├── misc ├── RdClass ├── RdClean.pl ├── RdDef ├── RdForb ├── RdMethod ├── RdSum ├── RdWpget ├── RdWpset ├── Rdck ├── compileman.R ├── gillespie.png ├── recreate_aamodels.R └── recreate_codonmodels.R └── pkg ├── .Rbuildignore ├── .Rinstignore ├── DESCRIPTION ├── NAMESPACE ├── R └── .gitignore ├── data └── .gitignore ├── inst ├── .gitignore └── extdata │ └── .gitignore ├── man ├── .gitignore ├── 000==.Alphabet.Rd ├── 000==.Process.Rd ├── Alphabet.Rd ├── AminoAcidAlphabet.Rd ├── AminoAcidSequence.Rd ├── AminoAcidSubst.Rd ├── AnyAlphabet.Rd ├── BinaryAlphabet.Rd ├── BinarySequence.Rd ├── BinarySubst.Rd ├── BrownianInsertor.Rd ├── BrownianPath.BrownianInsertor.Rd ├── CodonAlphabet.Rd ├── CodonSequence.Rd ├── CodonSubst.Rd ├── CodonUNREST.Rd ├── ContinuousDeletor.Rd ├── ContinuousInsertor.Rd ├── Debug.PhyloSim.Rd ├── DiscreteDeletor.Rd ├── DiscreteInsertor.Rd ├── ECMrest.Rd ├── ECMunrest.Rd ├── Event.Rd ├── F81.Rd ├── F84.Rd ├── FastFieldDeletor.Rd ├── GTR.Rd ├── GY94.Rd ├── GeneralDeletor.Rd ├── GeneralInDel.Rd ├── GeneralInsertor.Rd ├── GeneralSubstitution.Rd ├── HKY.Rd ├── JC69.Rd ├── JTT.Rd ├── JTT.dcmut.Rd ├── K80.Rd ├── K81.Rd ├── LG.Rd ├── Log.PhyloSim.Rd ├── MtZoa.Rd ├── NucleotideAlphabet.Rd ├── NucleotideSequence.Rd ├── PAM.Rd ├── PAM.dcmut.Rd ├── PSRoot.Rd ├── PSRootSummary.Rd ├── Perform.Event.Rd ├── PhyloSim.Rd ├── Process.Rd ├── QMatrix.Rd ├── Scale.QMatrix.Rd ├── Sequence.Rd ├── Simulate.PhyloSim.Rd ├── Site.Rd ├── T92.Rd ├── TN93.Rd ├── ToleranceSubstitution.Rd ├── Translate.CodonSequence.Rd ├── UNREST.Rd ├── Undocumented.PhyloSim.Rd ├── WAG.Rd ├── areSynonymous.CodonAlphabet.Rd ├── as.character.Alphabet.Rd ├── as.character.Event.Rd ├── as.character.GeneralSubstitution.Rd ├── as.character.PhyloSim.Rd ├── as.character.Process.Rd ├── as.character.QMatrix.Rd ├── as.character.Sequence.Rd ├── as.character.Site.Rd ├── as.character.ToleranceSubstitution.Rd ├── attachHookToNode.PhyloSim.Rd ├── attachProcess.Sequence.Rd ├── attachProcess.Site.Rd ├── attachSeqToNode.PhyloSim.Rd ├── buildFromPAML.AminoAcidSubst.Rd ├── buildFromPAML.CodonSubst.Rd ├── checkConsistency.Alphabet.Rd ├── checkConsistency.AminoAcidSubst.Rd ├── checkConsistency.BinarySubst.Rd ├── checkConsistency.BrownianInsertor.Rd ├── checkConsistency.CodonAlphabet.Rd ├── checkConsistency.CodonSequence.Rd ├── checkConsistency.CodonSubst.Rd ├── checkConsistency.CodonUNREST.Rd ├── checkConsistency.ContinuousDeletor.Rd ├── checkConsistency.ContinuousInsertor.Rd ├── checkConsistency.DiscreteDeletor.Rd ├── checkConsistency.DiscreteInsertor.Rd ├── checkConsistency.Event.Rd ├── checkConsistency.F81.Rd ├── checkConsistency.F84.Rd ├── checkConsistency.FastFieldDeletor.Rd ├── checkConsistency.GTR.Rd ├── checkConsistency.GY94.Rd ├── checkConsistency.GeneralDeletor.Rd ├── checkConsistency.GeneralInDel.Rd ├── checkConsistency.GeneralInsertor.Rd ├── checkConsistency.GeneralSubstitution.Rd ├── checkConsistency.HKY.Rd ├── checkConsistency.JC69.Rd ├── checkConsistency.K80.Rd ├── checkConsistency.K81.Rd ├── checkConsistency.PSRoot.Rd ├── checkConsistency.PSRootSummary.Rd ├── checkConsistency.PhyloSim.Rd ├── checkConsistency.Process.Rd ├── checkConsistency.QMatrix.Rd ├── checkConsistency.Sequence.Rd ├── checkConsistency.Site.Rd ├── checkConsistency.T92.Rd ├── checkConsistency.TN93.Rd ├── checkConsistency.ToleranceSubstitution.Rd ├── checkConsistency.UNREST.Rd ├── clearStates.Sequence.Rd ├── clone.GeneralSubstitution.Rd ├── clone.Process.Rd ├── clone.Sequence.Rd ├── clone.ToleranceSubstitution.Rd ├── copySubSequence.Sequence.Rd ├── cpREV.Rd ├── deleteSubSequence.Sequence.Rd ├── detachHookFromNode.PhyloSim.Rd ├── detachProcess.Sequence.Rd ├── detachProcess.Site.Rd ├── detachSeqFromNode.PhyloSim.Rd ├── enableVirtual.PSRoot.Rd ├── exportStatTree.PhyloSim.Rd ├── flagTotalRate.Site.Rd ├── generateInsert.GeneralInsertor.Rd ├── getAcceptBy.GeneralInDel.Rd ├── getAcceptWin.GeneralInsertor.Rd ├── getAlignment.PhyloSim.Rd ├── getAlignmentLength.PhyloSim.Rd ├── getAlphabet.GeneralSubstitution.Rd ├── getAlphabet.Process.Rd ├── getAlphabet.QMatrix.Rd ├── getAlphabet.Site.Rd ├── getAlphabet.ToleranceSubstitution.Rd ├── getAlphabets.Sequence.Rd ├── getAncestral.Sequence.Rd ├── getAncestral.Site.Rd ├── getBaseFreqs.F81.Rd ├── getBaseFreqs.F84.Rd ├── getBaseFreqs.GTR.Rd ├── getBaseFreqs.HKY.Rd ├── getBaseFreqs.K80.Rd ├── getBaseFreqs.K81.Rd ├── getBaseFreqs.TN93.Rd ├── getBigRate.Sequence.Rd ├── getBranchEvents.PhyloSim.Rd ├── getCodonFreqs.GY94.Rd ├── getComments.PSRoot.Rd ├── getCumulativeRates.Sequence.Rd ├── getCumulativeRatesFromRange.Sequence.Rd ├── getDeletionTolerance.Sequence.Rd ├── getDist.ContinuousDeletor.Rd ├── getDist.ContinuousInsertor.Rd ├── getEdge.PhyloSim.Rd ├── getEdges.PhyloSim.Rd ├── getEquDist.GeneralSubstitution.Rd ├── getEquDist.ToleranceSubstitution.Rd ├── getEventRate.GeneralSubstitution.Rd ├── getEventRate.QMatrix.Rd ├── getEventRate.ToleranceSubstitution.Rd ├── getEventRateAtSite.GeneralSubstitution.Rd ├── getEventRateAtSite.ToleranceSubstitution.Rd ├── getEvents.Sequence.Rd ├── getEvents.Site.Rd ├── getEventsAtSite.FastFieldDeletor.Rd ├── getEventsAtSite.GY94.Rd ├── getEventsAtSite.GeneralDeletor.Rd ├── getEventsAtSite.GeneralInsertor.Rd ├── getEventsAtSite.GeneralSubstitution.Rd ├── getEventsAtSite.Process.Rd ├── getEventsAtSite.ToleranceSubstitution.Rd ├── getGenerateBy.GeneralInsertor.Rd ├── getHandler.Event.Rd ├── getId.PhyloSim.Rd ├── getId.Process.Rd ├── getId.QMatrix.Rd ├── getId.Sequence.Rd ├── getInsertHook.GeneralInsertor.Rd ├── getInsertionTolerance.Sequence.Rd ├── getKappa.F84.Rd ├── getKappa.GY94.Rd ├── getLength.Sequence.Rd ├── getLengthParam1.FastFieldDeletor.Rd ├── getLengthParam2.FastFieldDeletor.Rd ├── getLogFile.PhyloSim.Rd ├── getLogLevel.PhyloSim.Rd ├── getMatrix.QMatrix.Rd ├── getMaxLength.ContinuousDeletor.Rd ├── getMaxLength.ContinuousInsertor.Rd ├── getMethodsList.PSRoot.Rd ├── getName.Event.Rd ├── getName.PhyloSim.Rd ├── getName.Process.Rd ├── getName.QMatrix.Rd ├── getName.Sequence.Rd ├── getNedges.PhyloSim.Rd ├── getNodes.PhyloSim.Rd ├── getNtips.PhyloSim.Rd ├── getOmegaScalingFactor.GY94.Rd ├── getOmegas.CodonSequence.Rd ├── getParameterAtSite.Process.Rd ├── getParameterAtSites.Sequence.Rd ├── getPhylo.PhyloSim.Rd ├── getPosition.Event.Rd ├── getProbs.DiscreteDeletor.Rd ├── getProbs.DiscreteInsertor.Rd ├── getProcess.Event.Rd ├── getProcess.QMatrix.Rd ├── getProcesses.Sequence.Rd ├── getProcesses.Site.Rd ├── getProposeBy.GeneralInDel.Rd ├── getQMatrix.GeneralSubstitution.Rd ├── getQMatrix.ToleranceSubstitution.Rd ├── getRate.Event.Rd ├── getRate.GeneralInDel.Rd ├── getRate.GeneralSubstitution.Rd ├── getRate.QMatrix.Rd ├── getRate.ToleranceSubstitution.Rd ├── getRateList.GeneralSubstitution.Rd ├── getRateList.QMatrix.Rd ├── getRateList.ToleranceSubstitution.Rd ├── getRateMultipliers.Sequence.Rd ├── getRateParam.F81.Rd ├── getRateParam.F84.Rd ├── getRateParam.GTR.Rd ├── getRateParam.HKY.Rd ├── getRateParam.K80.Rd ├── getRateParam.K81.Rd ├── getRateParam.T92.Rd ├── getRateParam.TN93.Rd ├── getRateParamList.F81.Rd ├── getRateParamList.F84.Rd ├── getRateParamList.GTR.Rd ├── getRateParamList.HKY.Rd ├── getRateParamList.K80.Rd ├── getRateParamList.K81.Rd ├── getRateParamList.T92.Rd ├── getRateParamList.TN93.Rd ├── getRootNode.PhyloSim.Rd ├── getRootSeq.PhyloSim.Rd ├── getScale.BrownianInsertor.Rd ├── getScaledMatrix.QMatrix.Rd ├── getSeqFromNode.PhyloSim.Rd ├── getSequence.Site.Rd ├── getSequences.PhyloSim.Rd ├── getSite.Event.Rd ├── getSiteSpecificParamIds.Process.Rd ├── getSiteSpecificParamList.Process.Rd ├── getSites.Sequence.Rd ├── getSize.Alphabet.Rd ├── getSizes.DiscreteDeletor.Rd ├── getSizes.DiscreteInsertor.Rd ├── getState.Site.Rd ├── getStates.Sequence.Rd ├── getString.Sequence.Rd ├── getSymbolFreqs.Sequence.Rd ├── getSymbolLength.Alphabet.Rd ├── getSymbols.Alphabet.Rd ├── getTableId.CodonAlphabet.Rd ├── getTemplateSeq.GeneralInsertor.Rd ├── getTheta.T92.Rd ├── getTipLabels.PhyloSim.Rd ├── getTips.PhyloSim.Rd ├── getToleranceMargin.FastFieldDeletor.Rd ├── getTotalRate.Site.Rd ├── getTotalRates.Sequence.Rd ├── getTotalRatesFromRange.Sequence.Rd ├── getTransTable.CodonAlphabet.Rd ├── getTreeLength.PhyloSim.Rd ├── getType.Alphabet.Rd ├── getType.BrownianInsertor.Rd ├── getType.FastFieldDeletor.Rd ├── getUniqueAlphabets.Sequence.Rd ├── getUniqueProcesses.Sequence.Rd ├── getWriteProtected.Alphabet.Rd ├── getWriteProtected.Event.Rd ├── getWriteProtected.Process.Rd ├── getWriteProtected.QMatrix.Rd ├── getWriteProtected.Sequence.Rd ├── globalConsistencyCheck.PSRoot.Rd ├── hasSiteSpecificParameter.Process.Rd ├── hasSymbols.Alphabet.Rd ├── hasUndefinedRate.GeneralInDel.Rd ├── hasUndefinedRate.GeneralSubstitution.Rd ├── hasUndefinedRate.Process.Rd ├── hasUndefinedRate.ToleranceSubstitution.Rd ├── insertSequence.Sequence.Rd ├── intersect.list.PSRoot.Rd ├── is.Alphabet.Rd ├── is.CodonAlphabet.Rd ├── is.CodonUNREST.Rd ├── is.Event.Rd ├── is.GY94.Rd ├── is.GeneralDeletor.Rd ├── is.GeneralInDel.Rd ├── is.GeneralInsertor.Rd ├── is.GeneralSubstitution.Rd ├── is.PSRoot.Rd ├── is.Process.Rd ├── is.QMatrix.Rd ├── is.Sequence.Rd ├── is.Site.Rd ├── is.ToleranceSubstitution.Rd ├── is.na.PSRoot.Rd ├── is.phylo.Rd ├── is.tip.PhyloSim.Rd ├── isAttached.Site.Rd ├── isEmpty.Alphabet.Rd ├── isStartCodon.CodonAlphabet.Rd ├── isStopCodon.CodonAlphabet.Rd ├── ll.PSRoot.Rd ├── mtArt.Rd ├── mtMam.Rd ├── mtREV24.Rd ├── my.all.equal.PSRoot.Rd ├── newAAMatrix.AminoAcidSubst.Rd ├── newMatrix.CodonSubst.Rd ├── omegaHist.CodonSequence.Rd ├── omegaVarM0.CodonSequence.Rd ├── omegaVarM1.CodonSequence.Rd ├── omegaVarM2.CodonSequence.Rd ├── omegaVarM3.CodonSequence.Rd ├── omegaVarM4.CodonSequence.Rd ├── plot.ContinuousDeletor.Rd ├── plot.ContinuousInsertor.Rd ├── plot.DiscreteDeletor.Rd ├── plot.DiscreteInsertor.Rd ├── plot.GeneralSubstitution.Rd ├── plot.PhyloSim.Rd ├── plot.Sequence.Rd ├── plot.ToleranceSubstitution.Rd ├── plotParametersAtSites.Sequence.Rd ├── plusGamma.Sequence.Rd ├── plusInvGamma.Sequence.Rd ├── print.PSRootSummary.Rd ├── print.QMatrix.Rd ├── proposeLength.GeneralInDel.Rd ├── readAlignment.PhyloSim.Rd ├── readTree.PhyloSim.Rd ├── rescaleQMatrix.GeneralSubstitution.Rd ├── rescaleQMatrix.ToleranceSubstitution.Rd ├── revComp.NucleotideSequence.Rd ├── sampleState.GeneralSubstitution.Rd ├── sampleState.ToleranceSubstitution.Rd ├── sampleStates.Sequence.Rd ├── saveAlignment.PhyloSim.Rd ├── scaleTree.PhyloSim.Rd ├── setAcceptBy.GeneralInDel.Rd ├── setAcceptWin.GeneralInsertor.Rd ├── setAlignment.PhyloSim.Rd ├── setAlphabet.GeneralSubstitution.Rd ├── setAlphabet.Process.Rd ├── setAlphabet.QMatrix.Rd ├── setAlphabet.Site.Rd ├── setAlphabet.ToleranceSubstitution.Rd ├── setAlphabets.Sequence.Rd ├── setAncestral.Sequence.Rd ├── setAncestral.Site.Rd ├── setBaseFreqs.F81.Rd ├── setBaseFreqs.F84.Rd ├── setBaseFreqs.GTR.Rd ├── setBaseFreqs.HKY.Rd ├── setBaseFreqs.K80.Rd ├── setBaseFreqs.K81.Rd ├── setBaseFreqs.TN93.Rd ├── setBigRate.Sequence.Rd ├── setBranchEvents.PhyloSim.Rd ├── setCodonFreqs.GY94.Rd ├── setComments.PSRoot.Rd ├── setCumulativeRates.Sequence.Rd ├── setDeletionTolerance.Sequence.Rd ├── setDist.ContinuousDeletor.Rd ├── setDist.ContinuousInsertor.Rd ├── setEdges.PhyloSim.Rd ├── setEquDist.GeneralSubstitution.Rd ├── setEquDist.ToleranceSubstitution.Rd ├── setEvents.Site.Rd ├── setGenerateBy.GeneralInsertor.Rd ├── setHandler.Event.Rd ├── setId.PhyloSim.Rd ├── setId.Process.Rd ├── setId.QMatrix.Rd ├── setId.Sequence.Rd ├── setInsertHook.GeneralInsertor.Rd ├── setInsertionTolerance.Sequence.Rd ├── setKappa.F84.Rd ├── setKappa.GY94.Rd ├── setLength.Sequence.Rd ├── setLengthParam1.FastFieldDeletor.Rd ├── setLengthParam2.FastFieldDeletor.Rd ├── setLogFile.PhyloSim.Rd ├── setLogLevel.PhyloSim.Rd ├── setMatrix.QMatrix.Rd ├── setMaxLength.ContinuousDeletor.Rd ├── setMaxLength.ContinuousInsertor.Rd ├── setMethodsList.PSRoot.Rd ├── setName.Event.Rd ├── setName.PhyloSim.Rd ├── setName.Process.Rd ├── setName.QMatrix.Rd ├── setName.Sequence.Rd ├── setNedges.PhyloSim.Rd ├── setNodes.PhyloSim.Rd ├── setNtips.PhyloSim.Rd ├── setOmegas.CodonSequence.Rd ├── setParameterAtSite.Process.Rd ├── setParameterAtSites.Sequence.Rd ├── setPhylo.PhyloSim.Rd ├── setPosition.Event.Rd ├── setProbs.DiscreteDeletor.Rd ├── setProbs.DiscreteInsertor.Rd ├── setProcess.Event.Rd ├── setProcess.QMatrix.Rd ├── setProcesses.Sequence.Rd ├── setProcesses.Site.Rd ├── setProposeBy.GeneralInDel.Rd ├── setQMatrix.GeneralSubstitution.Rd ├── setQMatrix.ToleranceSubstitution.Rd ├── setRate.Event.Rd ├── setRate.GY94.Rd ├── setRate.GeneralInDel.Rd ├── setRate.GeneralSubstitution.Rd ├── setRate.QMatrix.Rd ├── setRate.ToleranceSubstitution.Rd ├── setRateList.GeneralSubstitution.Rd ├── setRateList.QMatrix.Rd ├── setRateList.ToleranceSubstitution.Rd ├── setRateMultipliers.Sequence.Rd ├── setRateParam.F81.Rd ├── setRateParam.F84.Rd ├── setRateParam.GTR.Rd ├── setRateParam.HKY.Rd ├── setRateParam.K80.Rd ├── setRateParam.K81.Rd ├── setRateParam.T92.Rd ├── setRateParam.TN93.Rd ├── setRateParamList.F81.Rd ├── setRateParamList.F84.Rd ├── setRateParamList.GTR.Rd ├── setRateParamList.HKY.Rd ├── setRateParamList.K80.Rd ├── setRateParamList.K81.Rd ├── setRateParamList.T92.Rd ├── setRateParamList.TN93.Rd ├── setRootNode.PhyloSim.Rd ├── setRootSeq.PhyloSim.Rd ├── setScale.BrownianInsertor.Rd ├── setScaledMatrix.QMatrix.Rd ├── setSequence.Site.Rd ├── setSequences.PhyloSim.Rd ├── setSite.Event.Rd ├── setSiteSpecificParamIds.Process.Rd ├── setSiteSpecificParamList.Process.Rd ├── setSize.Alphabet.Rd ├── setSizes.DiscreteDeletor.Rd ├── setSizes.DiscreteInsertor.Rd ├── setState.Site.Rd ├── setStates.Sequence.Rd ├── setString.Sequence.Rd ├── setSymbolLength.Alphabet.Rd ├── setSymbols.Alphabet.Rd ├── setTableId.CodonAlphabet.Rd ├── setTemplateSeq.GeneralInsertor.Rd ├── setTheta.T92.Rd ├── setTipLabels.PhyloSim.Rd ├── setTips.PhyloSim.Rd ├── setToleranceMargin.FastFieldDeletor.Rd ├── setTotalRate.Site.Rd ├── setTotalRates.Sequence.Rd ├── setTransTable.CodonAlphabet.Rd ├── setTreeLength.PhyloSim.Rd ├── setType.Alphabet.Rd ├── setType.BrownianInsertor.Rd ├── setType.FastFieldDeletor.Rd ├── setUniqueAlphabets.Sequence.Rd ├── setUniqueProcesses.Sequence.Rd ├── setWriteProtected.Alphabet.Rd ├── setWriteProtected.Event.Rd ├── setWriteProtected.Process.Rd ├── setWriteProtected.QMatrix.Rd ├── setWriteProtected.Sequence.Rd ├── stringLength.Rd ├── stringLengthVector.Rd ├── summary.Alphabet.Rd ├── summary.AminoAcidSubst.Rd ├── summary.BinarySubst.Rd ├── summary.BrownianInsertor.Rd ├── summary.CodonAlphabet.Rd ├── summary.CodonSubst.Rd ├── summary.ContinuousDeletor.Rd ├── summary.ContinuousInsertor.Rd ├── summary.DiscreteDeletor.Rd ├── summary.DiscreteInsertor.Rd ├── summary.Event.Rd ├── summary.F81.Rd ├── summary.F84.Rd ├── summary.FastFieldDeletor.Rd ├── summary.GTR.Rd ├── summary.GY94.Rd ├── summary.GeneralDeletor.Rd ├── summary.GeneralInDel.Rd ├── summary.GeneralInsertor.Rd ├── summary.GeneralSubstitution.Rd ├── summary.HKY.Rd ├── summary.JC69.Rd ├── summary.K80.Rd ├── summary.K81.Rd ├── summary.PSRoot.Rd ├── summary.PhyloSim.Rd ├── summary.Process.Rd ├── summary.QMatrix.Rd ├── summary.Sequence.Rd ├── summary.Site.Rd ├── summary.T92.Rd ├── summary.TN93.Rd ├── summary.ToleranceSubstitution.Rd ├── summary.UNREST.Rd ├── translateCodon.CodonAlphabet.Rd └── virtualAssignmentForbidden.PSRoot.Rd └── vignettes ├── .gitignore ├── Makefile └── PhyloSim.Rnw /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbotond/phylosim/HEAD/.gitignore -------------------------------------------------------------------------------- /Alphabet.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbotond/phylosim/HEAD/Alphabet.R -------------------------------------------------------------------------------- /AminoAcidMatrices.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sbotond/phylosim/HEAD/AminoAcidMatrices.R 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