A major new release of Jalview, the Java Sequence Alignment Viewer, is now
available from http://www.jalview.org. Originally created by Michele Clamp
in 1997 and one of the world's most popular alignment viewers, it has been
heavily re-engineered for version 2.0.
The original Jalview's features included:
- efficient handling of very large alignments
- wide range of colourschemes for highlighting residues by property and
conservation
- sequence clustering and tree generation
- definition of sequence groups and alignment regions
- postscript and html output
- read and write a wide range of sequence alignment formats
Jalview version 2 has all the features of the original and more:
- Work with many alignments at once
- apply different colourschemes to different parts of an alignment
- Annotate alignments with text and secondary structure labels
- read and write trees in new hampshire format
- jalview archives to store the current view for reloading later
- flexible, WYSIWIG generation of figures and images
- PNG bitmaps for presentations
- EPS lineart for publications
- integrated alignment and secondary structure prediction via the web.
Jalview runs on recent versions of MS Windows, Mac OS X and Linux, and
is distributed as a stand-alone installation, Java webstart
application and as a Java 1.1 applet. The application version of
Jalview interfaces with web services for alignment and secondary
structure prediction hosted by the School of Life Sciences at the
University of Dundee.
The Jalview developers are Andrew Waterhouse, Jim Procter, David
Martin and Geoff Barton, based at the School of Life Sciences at the
University of Dundee, Scotland. The project is developed under the GPL
license, as part of the VAMSAS project funded by BBSRC - the UK's
Biotechnology and Biological Sciences Research Council.
Michele Clamp, James Cuff, Stephen M. Searle and Geoffrey
J. Barton. The Jalview Java alignment editor. Bioinformatics 20 426-427
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Subject: Jalview Version 2.0 is now available