Maj is an interactive graphical tool for viewing synchronized multiple and pairwise alignments for several organisms. It can simultaneously display a nucleotide-level text representation of a multiple alignment, PIP diagrams of the corresponding pairwise alignments, and various color-coded and/or hyperlinked annotations.
The applet below displays alignments of the E. coli K-12 genome with sequence data from eleven other enteric bacteria. It has two distinct viewing modes: the "wide" view corresponds roughly to the output from Enteric, while the "close-up" view includes some features from Menteric. Maj does not yet support a choice of different reference genomes at this time.
Note: This applet requires Java 1.2 (or higher). For best compatibility, Sun's Java Plug-in is recommended. Please see Installing the Java Plug-in for more information.