Readme.Rmd

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output: github_document
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<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
```
# msaR

[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/msaR)](https://cran.r-project.org/package=msaR)


msaR is a an [htmlwidgets](https://github.com/ramnathv/htmlwidgets) wrapper of the [BioJS MSA viewer](https://github.com/wilzbach/msa) javascript library. msa will pass alignments to the BioJS MSA. 


## Installation

You can install msaR from CRAN or github:

```{r gh-installation, eval = FALSE}
# CRAN
install.packages("msaR")
#github
devtools::install_github("zachcp/msaR")

```

## Example

This is a basic example which shows you how to solve a common problem:

```{r, eval=F}
library(msaR)

# read some sequences from a multiple sequence alignment file and display
seqfile <- system.file("sequences","AHBA.aln", package="msaR")
msaR(seqfile, seqlogo = T)
```

![](man/figures/msaR_screenshot.png)


All contributions are welcome! Please feel free to submit a pull request.


### Support and Suggestions
If you have any problem or suggestion please open an issue [here](https://github.com/zachcp/msaR/issues)


### License

This project is licensed under the [Boost Software License 1.0](https://github.com/wilzbach/msa/blob/master/LICENSE).

> Permission is hereby granted, free of charge, to any person or organization
> obtaining a copy of the software and accompanying documentation covered by
> this license (the "Software") to use, reproduce, display, distribute,
> execute, and transmit the Software, and to prepare derivative works of the
> Software, and to permit third-parties to whom the Software is furnished to
> do so, all subject to the following:

If you use the MSAViewer on your website, it solely requires you to link to us