GetAdequateManyReps     Parallel model adequacy test
GetAdequateSelac        Model adequacy simulation
GetFunctionality        Calculate functionality
GetMarginalAllGenes     Get marginal reconstruction all genes
GetPartitionOrder       Get data partiion order
GetSelacPhiCat          Phi rate category information under SELAC+gamma
GetSelacSiteLikelihoods
                        Calculate site likelihoods under SelAC
NucSimulator            Simulate DNA under General-Time Reversible
                        model
PlotEquilbriumCodonDistribution
                        Function to plot a distribution of frequencies
                        of codons given a 3d array of equilibrium
                        frequency matrices
PlotExpectedFitness     Function to plot a distribution of fitnesses
                        based on codon equilibrium freqs
PlotGeneSiteInfo        Function to plot info by site in a gene
PlotMutationFitnessSpectra
                        Plot fitness of mutations, weighted by
                        frequency of those mutations
PlotPerAAFitness        Function to plot a distribution of fitnesses W
                        or selection coefficients S for a given optimal
                        aa and other terms.
SelacHMMOptimize        Efficient optimization of a Hidden Markov SELAC
                        model
SelacHMMSimulator       Simulate DNA under the SELAC model
SelacOptimize           Efficient optimization of the SELAC model
SelacSimulator          Simulate DNA under the SELAC model
SelacSimulatorEvolvingRates
                        Simulate DNA under the SELAC model and evolving
                        rates
SelonHMMOptimize        Optimize parameters under the HMM SELON model
SelonOptimize           Optimize parameters under the SELON model
SelonSimulator          Simulate DNA under the SELON model
archosaur               Example archosaur dataset
non_zero_pos            Example datasets
yeast                   Example yeast dataset
