BCM Java Alignment Viewer

Image of Java Alignment Viewer logotype

About the Software

Authors: Elinor Karlsson and K. James Durbin

© 1997-2000 Baylor College of Medicine Human Genome Sequencing Center. All rights reserved.

The Java Alignment Viewer is a Java application that provides improved sequence alignment visualization for amino acid and nucleotide alignments. It is especially effective for large sequences.

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

Features of the Java Alignment Viewer are:

  • It is available as both an applet and an 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

Java Alignment Viewer readme


Click here to download the Java Alignment Viewer


For additional information, contact us at hgsc-web@bcm.edu