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Quasispecies Diversity

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("QSutils")):


To install this package, start R (version "4.4") 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 1.22.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-2
Depends R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods
Imports ape, stats, psych
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, ggplot2
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Imports Me longreadvqs
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Follow Installation instructions to use this package in your R session.

Source Package QSutils_1.22.0.tar.gz
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macOS Binary (x86_64) QSutils_1.22.0.tgz
macOS Binary (arm64) QSutils_1.22.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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