DOI: 10.18129/B9.bioc.ggmsa  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ggmsa.

Plot Multiple Sequence Alignment using 'ggplot2'

Bioconductor version: 3.17

A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.

Author: Lang Zhou [aut, cre], Guangchuang Yu [aut, ths] , Shuangbin Xu [ctb], Huina Huang [ctb]

Maintainer: Lang Zhou <nyzhoulang at>

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


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:



HTML R Script ggmsa
PDF   Reference Manual
Text   NEWS


biocViews Alignment, Annotation, MultipleSequenceAlignment, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License Artistic-2.0
Depends R (>= 4.1.0)
Imports Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree(>= 1.17.1)
Suggests ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0)
Depends On Me
Imports Me ggaligner, piglet
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ggmsa_1.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) ggmsa_1.6.0.tgz
macOS Binary (arm64) ggmsa_1.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: