This is the released version of scoup; for the devel version, see scoup.
Simulate Codons with Darwinian Selection Modelled as an OU ProcessBioconductor version: Release (3.21)
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 is built upon the fitness landscape paradigm of Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno. This enables realistic evolutionary process of living organisms to be reproducible 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 fitness landscape fluctuations on the inference of diversifying selection, may now be investigated with minimal effort. Frequency-dependent and stochastic fitness landscape update techniques are available.
Author: Hassan Sadiq [aut, cre, cph] ORCID: 0000-0003-0192-7134
Maintainer: Hassan Sadiq <hassan.t.sadiq at gmail.com>
Citation (from within R, entercitation("scoup")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scoup")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scoup")Follow Installation instructions to use this package in your R session.
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