queeems
This is the development version of queeems; for the stable release version, see queeems.
All Bioconductor versions of queeems
3.24 (devel), 3.23 (release)
Quantify the Extent of Evolutionary Evidence in Molecular Sequences
Bioconductor version: 3.24 · Package version: 1.1.1
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.
Author: Hassan Sadiq [aut, cre, cph, fnd] 
Maintainer: Hassan Sadiq <hassan.t.sadiq at gmail.com>
Citation
From within R, enter citation("queeems"):
Hassan Sadiq. queeems: Quantify the Extent of Evolutionary Evidence in Molecular Sequences. doi:10.18129/B9.bioc.queeems, R package version 1.1.1, https://bioconductor.org/packages/queeems.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("queeems")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.1 |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/thsadiq/queeems |
| Bug Reports | https://github.com/thsadiq/queeems/issues |
| Last updated | 2026-06-22 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2341 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Bayesian, Classification, DataImport, Genetics, MathematicalBiology, ResearchField, SequenceMatching, Sequencing, Software, StatisticalMethod, WorkflowStep |
| Package Short Url | https://bioconductor.org/packages/queeems/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("queeems")| queeems: Quantify the Extent of Evolutionary Evidence in Molecular Sequences | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | queeems_1.1.1.tar.gz |
| Windows binary (x86_64) | queeems_1.1.1.zip |
| macOS binary (arm64) | queeems_1.1.1.tgz |
| macOS binary (x86_64) | queeems_1.1.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/queeems |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/queeems |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0), Biostrings
Imports: gtools, Matrix, methods, stats
Suggests: BiocStyle, knitr, testthat (>= 3.0.0)