jbrowse-plugin-msaview

May 7, 2026 ยท View on GitHub

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

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

Publishing

just push a new tag using e.g.

pnpm version minor