<!-- README.md is generated from README.Rmd. Please edit that file -->
# ggmsa:a visual exploration tool for multiple sequence alignment and associated data <img src="man/figures/logo.png" height="140" align="right" />
[](https://github.com/YuLab-SMU/ggmsa)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://cran.r-project.org/web/licenses/Artistic-2.0)
<!-- badges: start -->
<!-- [](https://cran.r-project.org/package=ggmsa)-->
<!-- [](https://cran.r-project.org/package=ggmsa)-->
<!-- badges: end -->
`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`
``` r
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:
``` r
if (!requireNamespace("devtools", quietly=TRUE))
install.packages("devtools")
devtools::install_github("YuLab-SMU/ggmsa")
```
## :bulb: Quick Example
``` r
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()
```
<!-- -->
## :books: Learn more
Check out the guides for learning everything there is to know about all
the different features:
- [Getting
Started](https://yulab-smu.github.io/ggmsa/articles/ggmsa.html)
- [Annotations](https://yulab-smu.github.io/ggmsa/articles/guides/Annotations.html)
- [Color Schemes and Font
Families](https://yulab-smu.github.io/ggmsa/articles/guides/Color_schemes_And_Font_Families.html)
- [Theme](https://yulab-smu.github.io/ggmsa/articles/guides/MSA_theme.html)
- [Other
Modules](https://yulab-smu.github.io/ggmsa/articles/guides/Other_Modules.html)
- [View
Modes](https://yulab-smu.github.io/ggmsa/articles/guides/View_modes.html)
## :runner: Author
- [Guangchuang Yu](https://guangchuangyu.github.io) Professor, PI
- [Lang Zhou](https://github.com/nyzhoulang) Master’s Student
- [Shuangbin Xu](https://github.com/xiangpin) 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](https://github.com/YuLab-SMU/ggmsa/blob/master/CONDUCT.md).
