Package: scoup 1.1.0
Hassan Sadiq
scoup: Simulate Codons with Darwinian Selection Modelled as an OU Process
An elaborate molecular evolutionary framework that facilitates straightforward simulation of codon genetic sequences subjected to different degrees and/or patterns of Darwinian selection. The model was built upon the fitness landscape paradigm of Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno. This enabled realistic evolutionary process of living organisms to be reproduced seamlessly. For example, an Ornstein-Uhlenbeck fitness update algorithm is incorporated herein. Consequently, otherwise complex biological processes, such as the effect of the interplay between genetic drift and mutation on the inference of diversifying selection, may now be investigated with minimal effort. Frequency-dependent and deterministic fitness landscape update techniques are also available.
Authors:
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scoup.pdf |scoup.html✨
scoup/json (API)
NEWS
| # Install 'scoup' in R: |
| install.packages('scoup', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thsadiq/scoup/issues
On BioConductor:scoup-1.1.0(bioc 3.21)scoup-1.0.0(bioc 3.20)
alignmentclassificationcomparativegenomicsdataimportgeneticsmathematicalbiologyresearchfieldsequencingsequencematchingsoftwarestatisticalmethodworkflowstep
Last updated 16 days agofrom:23d89b3ce3. Checks:OK: 4 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 31 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
Exports:aaGammaaaGaussaaSCupdateaInfoalignsimasymMeanasymVarbiTreebranchLcodonCoeffscodonFreqcoeffscseqdetailsdiscreteInputdNdSdndsCalculatoreffpopfixMatrixfreqshbInputlscapenodesnsynVarouEvolveouInputphylogenyreversionsamplerseqCOLseqDetailsseqsseqWritershowsitessitesimsubsMatrixsynVartaxavNvSwInput
Dependencies:askpassBiocGenericsBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitelatticeMatrixmimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Obtain Gamma Distributed Amino Acid Selection Coefficients | aaGamma |
| Obtain Gaussian Distributed Amino Acid Selection Coefficients | aaGauss |
| Simulate Codon Sequence Alignment | aaSCupdate aaSCupdate.discrete aaSCupdate.ou alignsim alignsim.discrete alignsim.omega alignsim.ou effpop lscape nsynVar sampler sitesim sitesim.discrete sitesim.omega sitesim.ou vNvS |
| Amino Acid Selection Coefficients | aminoSC-class coeffs coeffs,aminoSC-method nsynVar,aminoSC-method show,aminoSC-method synVar synVar,aminoSC-method |
| Generate a Balanced Bifurcating Evolutionary Tree | biTree tree |
| Transform Amino Acid to Codon Selection Coefficients | codonCoeffs |
| Generate Codon Frequencies From Selection Coefficients | codonFreq |
| Codon Frequencies and Selection Coefficients | codonvalues-class coeffs,codonvalues-method freqs freqs,codonvalues-method show,codonvalues-method |
| Deterministic Simulation Model Input | aaSCupdate,discrete-method alignsim,discrete,seqParameters-method discrete-class effpop,discrete-method lscape,discrete-method sampler,discrete-method show,discrete-method sitesim,discrete,numeric-method |
| Populate Deterministic Seascape Model Parameters | discreteInput |
| Estimate dN/dS Value Analytically | dndsCalculator |
| Construct Fixation Rate Matrix | fixMatrix |
| Generate Halpern-Bruno Substitution Model Parameters | hbInput |
| Halpern-Bruno Mutation-Selection Evolutionary Model Input | effpop,hbParameters-method hbParameters-class nsynVar,hbParameters-method sampler,hbParameters-method show,hbParameters-method vNvS,hbParameters-method |
| Frequency-Dependent Evolutionary Model Specification | alignsim,omega,seqParameters-method effpop,omega-method lscape,omega-method nsynVar,omega-method omega-class sampler,omega-method show,omega-method sitesim,omega,numeric-method vNvS,omega-method |
| Ornstein-Uhlenbeck Stochastic Simulation Model Object | aaSCupdate,ou-method alignsim,ou,seqParameters-method asymMean asymMean,ou-method asymVar asymVar,ou-method ou-class reversion reversion,ou-method show,ou-method sitesim,ou,numeric-method |
| Simulate the Trend of an Ornstein-Uhlenbeck Process | ouEvolve |
| Populate Parameters of the Ornstein-Uhlenbeck Algorithm | ouInput |
| Simulate Codons with Darwinian Selection Added as an OU Process | scoup-package scoup |
| Output from the 'scoup::alignsim' Genetic Sequence Simulator | aInfo aInfo,scoup-method cseq cseq,scoup-method dNdS dNdS,scoup-method scoup-class seqCOL seqCOL,scoup-method seqs seqs,scoup-method show,scoup-method |
| Populate Sequence Alignment Information | seqDetails |
| Simulated Codon Sequence Structure | branchL branchL,seqParameters-method details details,seqParameters-method nodes nodes,seqParameters-method phylogeny phylogeny,seqParameters-method seqParameters-class show,seqParameters-method sites sites,seqParameters-method taxa taxa,seqParameters-method |
| Write Numeric Codon Alignment to a NEXUS File | seqWriter |
| Build Mutation-Selection Codon Substitution Matrix | subsMatrix |
| Populate Frequency-Dependent Simulation Model Parameters | wInput |
