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ggmsa:a visual exploration tool for multiple sequence alignment and associated data <img src="man/figures/logo.png" height="140" align="right" />

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ggmsa is designed for visualization and annotation of multiple sequence alignment. It implements functions to visualize publication-quality multiple sequence alignments (protein/DNA/RNA) in R extremely simple and powerful.

For details, please visit http://yulab-smu.top/ggmsa/

:hammer: Installation

The released version from Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ggmsa")

Alternatively, you can grab the development version from github using devtools:

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("YuLab-SMU/ggmsa")

:bulb: Quick Example

library(ggmsa)
protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")
ggmsa(protein_sequences, start = 221, end = 280, char_width = 0.5, seq_name = TRUE) + geom_seqlogo() + geom_msaBar()

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:books: Learn more

Check out the guides for learning everything there is to know about all the different features:

• Getting Started
• Annotations
• Color Schemes and Font Families
• Theme
• Other Modules
• View Modes

:runner: Author

• Guangchuang Yu Professor, PI
• Lang Zhou Master’s Student
• Shuangbin Xu PhD Student

YuLab https://yulab-smu.top/

Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University

:sparkling_heart: Contributing

We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.