Man pages for bomeara/selac
Selection Models for Amino Acid and/or Codon Evolution
| archosaur | Example archosaur dataset |
| 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 |
| internal | Internal functions |
| non_zero_pos | Example datasets |
| NucSimulator | Simulate DNA under General-Time Reversible model |
| PlotEquilbriumCodonDistribution | Function to plot a distribution of frequencies of codons... |
| PlotExpectedFitness | Function to plot a distribution of fitnesses based on codon... |
| PlotGeneSiteInfo | Function to plot info by site in a gene |
| PlotMutationFitnessSpectra | Plot fitness of mutations, weighted by frequency of those... |
| PlotPerAAFitness | Function to plot a distribution of fitnesses W or selection... |
| 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 |
| yeast | Example yeast dataset |
