QSutils
This is the released version of QSutils; for the devel version, see QSutils.
All Bioconductor versions of QSutils
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8
Quasispecies Diversity
Bioconductor version: 3.23 · Package version: 1.30.0
Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.
Author: Mercedes Guerrero-Murillo [cre, aut] 
, Josep Gregori i Font [aut]
Maintainer: Mercedes Guerrero-Murillo <mergumu at gmail.com>
Citation
From within R, enter citation("QSutils"):
Mercedes Guerrero-Murillo, Josep Gregori i Font. QSutils: Quasispecies Diversity. doi:10.18129/B9.bioc.QSutils, R package version 1.30.0, https://bioconductor.org/packages/QSutils.
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")
BiocManager::install("QSutils")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.30.0 |
| License | GPL-2 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| Downloads rank | 1119 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, DNASeq, DataImport, GeneticVariability, Genetics, SequenceMatching, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/QSutils/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("QSutils")| Quasispecies Data | HTML | R Script |
| Characterizing viral quasispecies | HTML | R Script |
| Simulating Quasispecies Composition | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | QSutils_1.30.0.tar.gz |
| Windows binary (x86_64) | QSutils_1.30.0.zip |
| macOS binary (arm64) | QSutils_1.30.0.tgz |
| macOS binary (x86_64) | QSutils_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/QSutils |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/QSutils |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods
Reverse dependencies
Imports Me (1): longreadvqs