Package: selac 1.7.5

Jeremy Beaulieu

selac: Selection Models for Amino Acid and/or Codon Evolution

Sets up and executes a SelAC model (Selection on Amino acids and codons) for testing the presence of selection in amino acid or codon among a set of genes on a fixed phylogeny. Beaulieu et al (2019) <doi:10.1093/molbev/msy222>.

Authors:Jeremy Beaulieu [aut, cre], JJ Chai [aut], Mike Gilchrist [aut], Cedric Landerer [aut], Graham Derryberry [aut], Brian O'Meara [aut]

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selac.pdf |selac.html✨
selac/json (API)

# Install 'selac' in R:
install.packages('selac', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bomeara/selac/issues

Datasets:

On CRAN:

2.65 score 1 stars 18 scripts 18 downloads 12 exports 34 dependencies

Last updated 3 years agofrom:cfa135e474. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winOKDec 19 2024
R-4.5-linuxOKDec 19 2024
R-4.4-winOKDec 19 2024
R-4.4-macOKDec 19 2024
R-4.3-winOKDec 19 2024
R-4.3-macOKDec 19 2024

Exports:GetAdequateManyRepsGetAdequateSelacGetFunctionalityGetMarginalAllGenesGetPartitionOrderGetSelacSiteLikelihoodsNucSimulatorSelacOptimizeSelacSimulatorSelacSimulatorEvolvingRatesSelonOptimizeSelonSimulator

Dependencies:ade4apeclicpp11data.tabledeSolvedigestexpmgenericsGenSAglueigraphlatticelifecyclemagrittrMASSMatrixnlmenloptrnnetphangornpixmappkgconfigquadprogRColorBrewerRcppRcppArmadillorlangsegmentedseqinrspstatmodvctrszoo

Readme and manuals

Help Manual

Help pageTopics
Parallel model adequacy testGetAdequateManyReps
Model adequacy simulationGetAdequateSelac
Calculate functionalityGetFunctionality
Get marginal reconstruction all genesGetMarginalAllGenes
Get data partiion orderGetPartitionOrder
Phi rate category information under SELAC+gammaGetSelacPhiCat
Calculate site likelihoods under SelACGetSelacSiteLikelihoods
Example datasetsnon_zero_pos
Simulate DNA under General-Time Reversible modelNucSimulator
Function to plot a distribution of frequencies of codons given a 3d array of equilibrium frequency matricesPlotEquilbriumCodonDistribution
Function to plot a distribution of fitnesses based on codon equilibrium freqsPlotExpectedFitness
Function to plot info by site in a genePlotGeneSiteInfo
Plot fitness of mutations, weighted by frequency of those mutationsPlotMutationFitnessSpectra
Function to plot a distribution of fitnesses W or selection coefficients S for a given optimal aa and other terms.PlotPerAAFitness
Example yeast datasetmodel.fit phy yeast yeast.gene
Efficient optimization of a Hidden Markov SELAC modelSelacHMMOptimize
Simulate DNA under the SELAC modelSelacHMMSimulator
Efficient optimization of the SELAC modelselac SelacOptimize
Simulate DNA under the SELAC modelSelacSimulator
Simulate DNA under the SELAC model and evolving ratesSelacSimulatorEvolvingRates
Example archosaur datasetarchosaur archosaur.phy uce.model.fit
Optimize parameters under the HMM SELON modelSelonHMMOptimize
Optimize parameters under the SELON modelSelonOptimize
Simulate DNA under the SELON modelSelonSimulator