# jbrowse-plugin-msaview

This plugin packages https://github.com/gmod/react-msaview for usage inside of
JBrowse 2

See the docs for the react-msaview for more info
https://github.com/GMOD/react-msaview/blob/main/docs/user_guide.md

## Gallery

![](img/1.png)

MSAView plugin running in JBrowse 2

## Demo

https://jbrowse.org/code/jb2/main/index.html?config=https://unpkg.com/jbrowse-plugin-msaview/dist/config.json&session=share-BVmmEYAoAv&password=SuQaN

## Features

- Vertical virtualized scrolling of phylogenetic tree
- Vertical and horizontal virtualized scrolling of multiple sequence alignment
- View metadata about alignment from MSA headers (e.g. stockholm)
- Collapse subtrees with click action on branches which also hides gaps that
  were introduced by that subtree in the rest of the alignment
- Allows "zooming out" by setting tiny rowHeight/colWidth settings
- Allows changing color schemes, with jalview, clustal, and other color schemes
- Allows toggling the branch length rendering for the phylogenetic tree
- Can share sessions with other users which will send relevant settings and
  links to files to automatically open your results
- The tree or the MSA panel can be loaded separately from each other

## File format supports

- FASTA formatted for MSA (e.g. gaps already inserted)
- Stockholm files (e.g. .stock file, with or without embedded newick tree, uses
  stockholm-js parser. also supports "multi-stockholm" files with multiple
  alignments embedded in a single file)
- Clustal files (e.g. .aln file, uses clustal-js parser)
- Newick (tree can be loaded separately as a .nh file)

## Publication

If you find this tool useful please cite our work

Diesh, C., Stevens, G., Bridge, C., Hogue, G., Buels, R., Cain, S., Stein, L., &
Holmes, I. (2026). Proteins in the Genome Browser: Integration of Phylogenies,
Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2. Journal
of Molecular Biology, 169645. https://doi.org/10.1016/j.jmb.2026.169645

See also https://github.com/GMOD/proteinbrowser for overview

## Availability

This plugin is installed by default on https://genomes.jbrowse.org so you can
use it on any species there

## Programmatic usage

See [DEVELOPERS.md](DEVELOPERS.md)

## Publishing

just push a new tag using e.g.

```
pnpm version minor
```