Package: queeems
Version: 1.0.0
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: <hassan.t.sadiq@gmail.com>
URL: https://github.com/thsadiq/queeems
BugReports: https://github.com/thsadiq/queeems/issues
Packaged: 2026-04-30 06:05:35 UTC; root
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:07:17 UTC
RemoteUrl: https://github.com/bioc/queeems
RemoteRef: RELEASE_3_23
RemoteSha: c33f2089d26db47476a442545c68d5f78ebdc458
NeedsCompilation: no
Author: Hassan Sadiq [aut, cre, cph, fnd] (ORCID:
    <https://orcid.org/0000-0003-0192-7134>)
Maintainer: Hassan Sadiq <hassan.t.sadiq@gmail.com>
Built: R 4.6.0; ; 2026-04-30 06:07:00 UTC; windows
