AlignmentViewer: Sequence Analysis of Large Protein Families

F1000Res. 2020 Mar 27;9:ISCB Comm J-213. doi: 10.12688/f1000research.22242.2. eCollection 2020.


AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via

Keywords: JavaScript; MSA; alignment viewer; protein alignments; tool; web-based.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Humans
  • Proteins* / genetics
  • Sequence Alignment*
  • Sequence Analysis, Protein
  • Software*
  • Web Browser


  • Proteins