Global functions | |
---|---|
BrownianEvolveParameters | Source code |
CalculatePolynomialCoefficients | Source code |
CodonNumericToString | Source code |
CodonStringToCharacter | Source code |
CodonStringToNumeric | Source code |
CompareVectors | Man page Source code |
ComputeEquilibriumAAFitness | Source code |
ComputeEquilibriumCodonFrequencies | Source code |
ComputeMutationFitnesses | Source code |
ComputeMutationFitnessesUnderGammaRates | Source code |
ComputeStartingBranchLengths | Source code |
ConvertCodonNumericDataToAAData | Source code |
CreateAADistanceMatrix | Man page Source code |
CreateAADistanceMatrixOriginal | Source code |
CreateAAFixationMatrix | Man page Source code |
CreateAAFixationMatrixForEverything | Source code |
CreateCodonFixationProbabilityMatrix | Source code |
CreateCodonFixationRateMatrix | Man page |
CreateCodonMutationMatrix | Man page Source code |
CreateCodonMutationMatrixGY94 | Source code |
CreateCodonMutationMatrixIndex | Source code |
CreateCodonMutationMatrixIndexEvolveAA | Source code |
CreateCodonMutationMatrixMutSel | Source code |
CreateCodonMutationMatrixYN98 | Source code |
CreateCodonSets | Source code |
CreateHMMNucleotideMutationMatrix | Source code |
CreateNucleotideDistanceMatrix | Source code |
CreateNucleotideMutationMatrix | Man page Source code |
CreateNucleotideMutationMatrixHMMSpecial | Source code |
CreateNucleotideMutationMatrixSpecial | Source code |
CreatePolynomialMatrix | Source code |
DNAbinToCodonCharacter | Source code |
DNAbinToCodonNumeric | Source code |
DNAbinToNucleotideCharacter | Source code |
DNAbinToNucleotideNumeric | Source code |
DiscreteGamma | Source code |
FastCreateAllCodonFixationProbabilityMatrices | Source code |
FastCreateAllCodonFixationProbabilityMatricesSetToOne | Source code |
FastCreateEvolveAACodonFixationProbabilityMatrix | Source code |
FastCreateOptAATransitionMatrices | Source code |
FindBranchGenerations | Source code |
FinishLikelihoodCalculation | Source code |
FinishLikelihoodCalculationHMM | Source code |
GenerateAAProperties | Source code |
GetAADistanceStartingParameters | Source code |
GetAAFreqsByGene | Source code |
GetAALikelihoodPerSite | Source code |
GetAdequateManyReps | Man page Source code |
GetAdequateSelac | Man page Source code |
GetAveAAPerSite | Source code |
GetBranchLikeAcrossAllSites | Source code |
GetBranchLikeAcrossAllSitesGTR | Source code |
GetCAI | Source code |
GetCodonFreqsByAA | Source code |
GetCodonFreqsByGene | Source code |
GetCodonFreqsByGeneHMM | Source code |
GetExpQt | Source code |
GetFMutSelSimulateInfo | Source code |
GetFitness | Source code |
GetFitnessStartingValues | Source code |
GetFunctionality | Man page Source code |
GetFunctionalityModelAdequacy | Source code |
GetGainLossRatios | Source code |
GetGeneSiteInfo | Source code |
GetGtrSimulateInfo | Source code |
GetIntervalSequencesAllSites | Source code |
GetKnownFunctionality | Source code |
GetLikelihood | Source code |
GetLikelihoodGY94_YN98_CodonForManyCharGivenAllParams | Source code |
GetLikelihoodHMMUCEForManyCharVaryingBySite | Source code |
GetLikelihoodMutSel_CodonForManyCharGivenAllParams | Source code |
GetLikelihoodMutSel_CodonForManyCharVaryingBySite | Source code |
GetLikelihoodNucleotideForManyCharGivenAllParams | Source code |
GetLikelihoodNucleotideForManyCharVaryingBySite | Source code |
GetLikelihoodSAC_AAForSingleCharGivenOptimum | Man page Source code |
GetLikelihoodSAC_CodonForManyCharGivenAllParams | Source code |
GetLikelihoodSAC_CodonForManyCharGivenAllParamsEvolvingAA | Source code |
GetLikelihoodSAC_CodonForManyCharGivenFixedOptimumAndQAndRoot | Source code |
GetLikelihoodSAC_CodonForManyCharVaryingBySite | Source code |
GetLikelihoodSAC_CodonForManyCharVaryingBySiteEvolvingAA | Source code |
GetLikelihoodSAC_CodonForSingleCharGivenOptimum | Source code |
GetLikelihoodSAC_CodonForSingleCharGivenOptimumHMMScoring | Source code |
GetLikelihoodUCEForManyCharGivenAllParams | Source code |
GetLikelihoodUCEForManyCharVaryingBySite | Source code |
GetLikelihoodUCEForSingleCharGivenOptimum | Source code |
GetLikelihoodUCEHMMForManyCharGivenAllParams | Source code |
GetLikelihoodUCEHMMForSingleCharGivenOptimum | Source code |
GetMarginalAllGenes | Man page Source code |
GetMarginalGene | Source code |
GetMarginalSingleSite | Source code |
GetMatrixAANames | Source code |
GetMaxName | Source code |
GetMaxNameUCE | Source code |
GetNucleotideFixationHMMMatrix | Source code |
GetNucleotideFixationMatrix | Source code |
GetNucleotideNucleotideDistance | Source code |
GetOptimalAAPerSite | Source code |
GetOptimalNucPerSite | Source code |
GetPairwiseNucleotideWeightSingleSite | Source code |
GetPairwiseProteinFixationProbabilityArbitraryLength | Man page Source code |
GetPairwiseProteinFixationProbabilitySingleSite | Man page Source code |
GetPartitionOrder | Man page Source code |
GetPhiLikelihoodPerSite | Source code |
GetProteinProteinDistance | Man page Source code |
GetSelacPhiCat | Man page Source code |
GetSelacSimulateInfo | Source code |
GetSelacSiteLikelihoods | Man page Source code |
GetTipIntervalStateSingleSite | Source code |
Laguerre | Source code |
LaguerreQuad | Source code |
LineMutationFitnessSpectra | Source code |
LogNormalQuad | Source code |
MakeDataArray | Source code |
MakeParameterArray | Source code |
MakeParameterArrayGTR | Source code |
NucSimulator | Man page Source code |
NucleotideStringToCharacter | Source code |
NucleotideStringToNumeric | Source code |
OUEvolveParameters | Source code |
OptimizeAllGenesGenericUCE | Source code |
OptimizeAllGenesNeUCE | Source code |
OptimizeAlphaBetaGtrOnly | Source code |
OptimizeEdgeLengths | Source code |
OptimizeEdgeLengthsGTRNew | Source code |
OptimizeEdgeLengthsUCENew | Source code |
OptimizeModelParsAlphaBetaGtrFixed | Source code |
OptimizeModelParsLarge | Source code |
OptimizeModelParsUCE | Source code |
OptimizeNucAllGenesUCE | Source code |
PlotBubbleMatrix | Source code |
PlotBubbleRatio | Source code |
PlotEquilbriumCodonDistribution | Man page Source code |
PlotExpectedFitness | Man page Source code |
PlotGeneSiteInfo | Man page Source code |
PlotMutationFitnessSpectra | Man page Source code |
PlotPerAAFitness | Man page Source code |
PlotTransitionNetwork | Source code |
PolynomialTransform | Source code |
PositionSensitivityMultiplierNormal | Source code |
PositionSensitivityMultiplierQuadratic | Source code |
PositionSensitivityMultiplierSigmoid | Source code |
SelacHMMOptimize | Man page Source code |
SelacHMMSimulator | Man page Source code |
SelacOptimize | Man page Source code |
SelacSimulator | Man page Source code |
SelacSimulatorEvolvingRates | Man page Source code |
SelonHMMOptimize | Man page Source code |
SelonOptimize | Man page Source code |
SelonSimulator | Man page Source code |
SingleBranchCalculation | Source code |
SingleSiteUpPass | Source code |
SingleSiteUpPassEvolvingRates | Source code |
SingleSiteUpPassHMM | Source code |
SitePattern | Source code |
TranslateCodon | Man page Source code |
TreeTraversalODE | Source code |
add.alpha | Source code |
archosaur | Man page |
archosaur.phy | Man page |
exp_A_tvec_codon | Source code |
expm_squaring | Source code |
findRoots | Source code |
internal_expAtv | Source code |
model.fit | Man page |
nChooseK | Source code |
non_zero_pos | Man page |
phy | Man page |
print.selac | Source code |
print.selon | Source code |
rep.row | Source code |
selac | Man page |
uce.model.fit | Man page |
yeast | Man page |
yeast.gene | Man page |
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