This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see QSutils.

Quasispecies Diversity

Bioconductor version: 3.18

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")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

QSUtils-Alignment HTML R Script
QSutils-Diversity HTML R Script
QSutils-Simulation HTML R Script
Reference Manual PDF


biocViews Alignment, DNASeq, DataImport, GeneticVariability, Genetics, SequenceMatching, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License file LICENSE
Depends R (>= 3.5), Biostrings, BiocGenerics, methods
Imports ape, stats, psych
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, ggplot2
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Depends On Me
Imports Me longreadvqs
Suggests Me
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Follow Installation instructions to use this package in your R session.

Source Package QSutils_1.20.0.tar.gz
Windows Binary QSutils_1.20.0.zip
macOS Binary (x86_64) QSutils_1.20.0.tgz
macOS Binary (arm64) QSutils_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/QSutils
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/QSutils
Bioc Package Browser https://code.bioconductor.org/browse/QSutils/
Package Short Url https://bioconductor.org/packages/QSutils/
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