README.md

msa-vis

Introduction

msa-vis is developed to generate publication-grade visualizations for multiple sequence alignments (MSA).

Getting started

The source code and required dependencies are containerized as a single image file that can be downloaded via Docker or Singularity.

Docker

docker pull jimmyliu1326/msa-vis

Singularity

singularity pull docker://jimmyliu1326/msa-vis

Once the image has been downloaded, try calling msa-vis.R to print the script usage message to screen.

Docker

docker run jimmyliu1326/msa-vis msa-vis.R --help

Singularity

singularity exec msa-vis.sif msa-vis.R --help

If the help message successfully prints to screen, then you are all set! 🥳

Example visualizations

DNA alignment

Amino acid alignment

Credit

msa-vis would not have been possible without the following open source packages developed by the amazing R community:

• ggmsa
• ggpubr
• scales
• furrr
• Biostrings