Package: queeems Version: 1.1.1 Date: 2025-04-28 License: GPL-3 + file LICENSE Authors@R: c(person("Hassan", "Sadiq", role=c("aut","cre","cph","fnd"), email="hassan.t.sadiq@gmail.com", comment=c(ORCID="0000-0003-0192-7134"))) Title: Quantify the Extent of Evolutionary Evidence in Molecular Sequences Description: Biological inferences obtained from molecular data are only as good as the extent of evolutionary signatures retained in the genetic data. Techniques available to quantify these signatures are largely targeted towards phylogeny reconstruction and they often rely on adhoc hypothesis tests of significance. I present a Bayesian function that assesses whether a set of genetic sequences are saturated. That is, it is useful for determining whether the evolutionary information in the sequences has eroded with time. Site specific Bayes factors are generated with respect to codon bases to allow for straightforward applications in extensive computational biology inquiries, including natural selection analyses. Depends: R (>= 4.5.0), Biostrings Imports: gtools, Matrix, methods, stats Suggests: BiocStyle, knitr, testthat (>= 3.0.0) VignetteBuilder: knitr Config/testthat/edition: 3 biocViews: Alignment, Bayesian, Classification, DataImport, Genetics, MathematicalBiology, ResearchField, Sequencing, SequenceMatching, Software, StatisticalMethod, WorkflowStep Contact: URL: https://github.com/thsadiq/queeems BugReports: https://github.com/thsadiq/queeems/issues Packaged: 2026-06-22 22:08:19 UTC; root Config/pak/sysreqs: zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-06-22 18:09:20 UTC RemoteUrl: https://github.com/bioc/queeems RemoteRef: HEAD RemoteSha: ed4991724b2f2b4e82c661760e110d627cfcb37a NeedsCompilation: no Author: Hassan Sadiq [aut, cre, cph, fnd] (ORCID: ) Maintainer: Hassan Sadiq