archosaur	archosaur
archosaur.phy	archosaur
CompareVectors	internal
CreateAADistanceMatrix	internal
CreateAAFixationMatrix	internal
CreateCodonFixationRateMatrix	internal
CreateCodonMutationMatrix	internal
CreateNucleotideMutationMatrix	internal
GetAdequateManyReps	GetAdequateManyReps
GetAdequateSelac	GetAdequateSelac
GetFunctionality	GetFunctionality
GetLikelihoodSAC_AAForSingleCharGivenOptimum	internal
GetMarginalAllGenes	GetMarginalAllGenes
GetPairwiseProteinFixationProbabilityArbitraryLength	internal
GetPairwiseProteinFixationProbabilitySingleSite	internal
GetPartitionOrder	GetPartitionOrder
GetProteinProteinDistance	internal
GetSelacPhiCat	GetSelacPhiCat
GetSelacSiteLikelihoods	GetSelacSiteLikelihoods
model.fit	yeast
NucSimulator	NucSimulator
phy	yeast
PlotEquilbriumCodonDistribution	PlotEquilbriumCodonDistribution
PlotExpectedFitness	PlotExpectedFitness
PlotGeneSiteInfo	PlotGeneSiteInfo
PlotMutationFitnessSpectra	PlotMutationFitnessSpectra
PlotPerAAFitness	PlotPerAAFitness
selac	SelacOptimize
SelacOptimize	SelacOptimize
SelacSimulator	SelacSimulator
SelacSimulatorEvolvingRates	SelacSimulatorEvolvingRates
SelonOptimize	SelonOptimize
SelonSimulator	SelonSimulator
TranslateCodon	internal
uce.model.fit	archosaur
yeast	yeast
yeast.gene	yeast
