API for bomeara/selac
Selection Models for Amino Acid and/or Codon Evolution

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
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
DiagArray Source code
DiscreteGamma Source code
FastCreateAllCodonFixationProbabilityMatrices Source code
FastCreateAllCodonFixationProbabilityMatricesSetToOne Source code
FastCreateEvolveAACodonFixationProbabilityMatrix Source code
FastCreateOptAATransitionMatrices 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
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_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
NucSimulator Man page Source code
NucleotideStringToCharacter Source code
NucleotideStringToNumeric Source code
OUEvolveParameters Source code
OptimizeAlphaBetaGtrOnly Source code
OptimizeEdgeLengths Source code
OptimizeEdgeLengthsUCE Source code
OptimizeModelParsAlphaBetaGtrFixed Source code
OptimizeModelParsLarge Source code
OptimizeModelParsUCE Source code
OptimizeNucAllGenesUCE Source code
PlotBubbleMatrix Source code
PlotBubbleRatio Source code
PlotEquilbriumCodonDistribution Source code
PlotExpectedFitness Source code
PlotGeneSiteInfo Source code
PlotMutationFitnessSpectra Source code
PlotPerAAFitness Source code
PlotTransitionNetwork Source code
PolynomialTransform Source code
PositionSensitivityMultiplierNormal Source code
PositionSensitivityMultiplierQuadratic Source code
PositionSensitivityMultiplierSigmoid Source code
SelacHMMOptimize Man page Source code
SelacHMMSimulator 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
SingleSiteUpPass Source code
SingleSiteUpPassEvolvingRates Source code
SingleSiteUpPassHMM Source code
SitePattern Source code
TranslateCodon Man page Source code
TreeTraversalODE Source code
add.alpha Source code
findRoots Source code
nChooseK Source code
phy Man page
print.selac Source code
print.selon Source code
rep.row Source code
yeast Man page
yeast.gene Man page
bomeara/selac documentation built on Dec. 15, 2017, 9:47 p.m.