Jalview

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Jalview is a multiple sequence alignment editor & viewer written in the Java programming language. It is used widely in a variety of web pages (e.g. the EBI ClustalW server and the Pfam protein domain database) but is available as a general purpose alignment editor.

Jalview
Developer: Waterhouse A, Procter J, Barton G, Martin D.
(Dundee University)
Original Version by Clamp M, Cuff J, Searle S, Barton G
OS: UNIX, Linux, Mac, MS-Windows
Use: Bioinformatics tool
Licence: LGPL
Website: http://www.jalview.org

Use Jalview for:

  • Viewing
    • Reads and writes alignments in a variety of formats (Fasta, PFAM, MSF, Clustal, BLC, PIR)
      • Save alignments and associated trees in Jalview XML format.
  • Editing
    • Gaps can be inserted/deleted using the mouse or keyboard.
    • Group editing (insertion deletion of gaps in groups of sequences).
    • Removal of gapped columns.
  • Analysis
    • Align sequences using Web Services (Clustal, Muscle...)
    • Amino acid conservation analysis similar to that of AMAS.
    • Alignment sorting options (by name, tree order, percent identity, group).
    • UPGMA and NJ trees calculated and drawn based on percent identity distances.
    • Sequence clustering using principal component analysis.
    • Removal of redundant sequences.
    • Smith Waterman pairwise alignment of selected sequences.
  • Annotation
    • Use web based secondary structure prediction programs (JNet).
  • Annotation
    • User predefined or custom colour schemes to colour alignments or groups.
    • Sequence feature retrieval and display on the alignment.
  • Publishing
    • Print your alignment with colours and annotations.
    • Create HTML pages.
    • Output alignment as portable network graphics image (PNG).
    • Output alignment as encapsulated postscript file (EPS).
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