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

ComputeEquilibriumCodonFrequenciesFunction to plot frequency of distribution of different Wi...
GetAdequateManyRepsParallel model adequacy test
GetAdequateSelacModel adequacy simulation
GetFunctionalityCalculate functionality
GetMarginalAllGenesGet marginal reconstruction all genes
GetPartitionOrderGet data partiion order
GetSelacPhiCatPhi rate category information under SELAC+gamma
GetSelacSiteLikelihoodsCalculate site likelihoods under SelAC
internalInternal functions
NucSimulatorSimulate DNA under General-Time Reversible model
PlotEquilbriumCodonDistributionFunction to plot a distribution of frequencies of codons...
PlotExpectedFitnessFunction to plot a distribution of fitnesses based on codon...
PlotGeneSiteInfoFunction to plot info by site in a gene
PlotMutationFitnessSpectraPlot fitness of mutations, weighted by frequency of those...
PlotPerAAFitnessFunction to plot a distribution of fitnesses W or selection...
SelacHMMOptimizeEfficient optimization of a Hidden Markov SELAC model
SelacHMMSimulatorSimulate DNA under the SELAC model
SelacOptimizeEfficient optimization of the SELAC model
SelacSimulatorSimulate DNA under the SELAC model
SelacSimulatorEvolvingRatesSimulate DNA under the SELAC model and evolving rates
SelonHMMOptimizeOptimize parameters under the HMM SELON model
SelonOptimizeOptimize parameters under the SELON model
SelonSimulatorSimulate DNA under the SELON model
yeastExample datasets
bomeara/selac documentation built on Sept. 22, 2018, 1:14 p.m.