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• Jalview

• Applet
• Application

• "The Jalview Java
  Alignment Editor,"
  
Bioinformatics, 12, 426-7

• Jalview 2

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Jalview is a multiple alignment editor written in java. 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.

Version 2.0 is the latest release version of Jalview. This version has many new features compared to the original version.

The original version of Jalview, version 1.18, can still be downloaded. Some features no longer work.

Jalview Features -- See major new developments by trying Jalview Version 2 --

• Sequence feature retrieval and display on the alignment
• Reads and writes alignments in a variety of formats
• Gaps can be inserted/deleted using the mouse.
• Conservation analysis similar to that of AMAS
• Group editing (insertion deletion of gaps in groups of sequences).
• Removal of gapped columns
• Many different colour schemes
• Alignment sorting options (by name, tree order, percent identity, group)
• Linking of group colours between the alignment, tree and PCA windows.
• 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
• EPS, PNG files can be generated for inclusion in documents

Special thanks go to Alex Bateman and the Pfam team for using Jalview and making many helpful suggestions

New JalView development has been funded for three years from 1st October 2004 by the BBSRC as part of the "Visualisation and Analysis of Biological Sequences, Alignments and Structures" Project. This project is coordinated by Geoff Barton at the University of Dundee with partners at EBI and BioSS and consultancy (blessing :-) from Michele Clamp; the originator of JalView.