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| Elinor Karlsson, James Durbin
The
Java Alignment Viewer is a new Java application that provides
improved sequence alignment visualization for aminoacid and
nucleotide alignments. It is especially effective for large
sequences.
README
for JAV
Download the JAV.tar
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It was developed to assist researchers in analyzing the output of
sequence alignment tools. Reading a FASTA formatted file, it displays
both nucleotide and protein alignments in two scrollable panels, one
that displays a scalable overview of the alignment and a second panel
showing the alignment at the nucleotide/amino acid level.
It is available as both an applet that runs inside a browser, and
as application. The application includes additional functionality
and uses Java Swing. See a screenshot
of the application
The Coolest Features of the Java Alignment Viewer are:
- It is available as an applet and application
- It displays synchronized overview and zoom panels of the sequence
- It handles very large protein and DNA alignment files (tested
up to 200,000 bases in length, with at least 10 sequences displayed)
- Spaces can be added and deleted from the sequence
- Changes to the sequence can be saved to disk
- Coloring schemes can be added by the user to the application
For additional information contact James Durbin at kdurbin@bcm.tmc.edu
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