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

MSAView plugin running in v1.5.0 of JBrowse web

Demo

https://s3.amazonaws.com/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)