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This is the development version of ggmsa; for the stable release version, see ggmsa.

Plot Multiple Sequence Alignment using 'ggplot2'

Bioconductor version: Development (3.20)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

ggmsa HTML R Script
Reference Manual PDF


biocViews Alignment, Annotation, MultipleSequenceAlignment, Software, Visualization
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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)
System Requirements
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Suggests ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0)
Linking To
Depends On Me
Imports Me ggaligner, SeedMatchR
Suggests Me
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Follow Installation instructions to use this package in your R session.

Source Package ggmsa_1.11.0.tar.gz
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macOS Binary (x86_64) ggmsa_1.11.0.tgz
macOS Binary (arm64) ggmsa_1.11.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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