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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" 2 "http://www.w3.org/TR/html4/loose.dtd"> 3<html> 4<head> 5<title>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</title> 6<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> 7<meta http-equiv="Content-Style-Type" content="text/css"> 8<link rel="stylesheet" type="text/css" href="gmaj.css"> 9</head> 10<body> 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> 84</body> 85</html>