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 5<title>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</title>
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11<p class=vvlarge>
12<h2>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</h2>
13<p class=vvlarge>
14Gmaj is a tool designed for viewing and manipulating Generalized
15Multiple Alignments (GMAs) produced by sequence-symmetric alignment
16programs such as <a href="http://www.bx.psu.edu/miller_lab/">TBA</a>
17(though it can also be used with MAF format alignments from other
18sources).  It can display interactive graphical and text
19representations of the alignments, diagrams showing the locations
20of exons and repeats, and other annotations -- all with the user's
21choice of reference sequence.
22<p>
23The program is written in Java in order to provide a graphical
24user interface that is portable across a variety of computer
25platforms; indeed its name stands for "Generalized Multiple
26Alignments with Java".  It requires <b>Java 1.3 or higher</b>,
27and for best compatibility
28<a href="http://java.com/en/download/manual.jsp">Sun's JRE</a>
29(or JDK) is recommended.
30<p>
31Gmaj can be run in two different modes: as a stand-alone
32application (for viewing local data files yourself) or as an
33applet over the world-wide web (to display your data on a server
34for viewing by others).  These modes are mostly similar, but
35have a few minor differences due to the underlying capabilities
36of applets vs. applications in Java.
37<p>
38<blockquote class=notop>
39<a href="http://globin.bx.psu.edu/java/gmaj/demo.html"
40>Applet demo</a>
41</blockquote>
42<p class=large>
43The current Gmaj distribution package is available for download
44as a compressed zip archive,
45<code><a href="http://globin.bx.psu.edu/dist/gmaj/gmaj.zip"
46>gmaj.zip</a></code>.
47<p>
48The following additional documentation files are included:
49<ul>
50<li>	<a href="gmaj_news.html">What's New in Gmaj</a><br>
51	A summary of the changes in each released version of Gmaj.
52	(Note important <b>bug fix</b> on 2005-Sep-13.)
53<p>
54<li>	<a href="gmaj_bugs.html">Known Bugs in Gmaj</a><br>
55	A discussion of the known bugs and anomalies we have
56	observed, but not yet resolved.  Some of these may depend
57	on your computer platform and/or version of Java.
58<p>
59<li>	<a href="gmaj_install.html">Installing Gmaj</a><br>
60	Describes how to unpack and set up Gmaj, for both
61	stand-alone and applet use.
62<p>
63<li>	<a href="gmaj_help.html">Starting and Running Gmaj</a><br>
64	Describes how to start Gmaj and use the GUI, in both
65	stand-alone and applet modes.  This is the file that Gmaj's
66	"Help - Manual" menu item points to.
67<p>
68<li>	<a href="gmaj_input.html">Input Files for Gmaj</a><br>
69	Detailed descriptions of the input files used by Gmaj, and
70	their formats.
71<p>
72<li>	<code><a href="sample.gmaj">sample.gmaj</a></code><br>
73	A sample template for the parameters file that tells Gmaj
74	which data files to load, among other things.  Includes
75	explanatory comments at the bottom.  This file is optional
76	if you don't want to display any annotations or use the
77	other features it provides.
78</ul>
79<p>
80
81<p class=vvlarge>
82<hr>
83<i>Cathy Riemer, June 2008</i>
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