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86 lines
3.3 KiB
HTML
86 lines
3.3 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
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"http://www.w3.org/TR/html4/loose.dtd">
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<html>
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<head>
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<title>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
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<meta http-equiv="Content-Style-Type" content="text/css">
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<link rel="stylesheet" type="text/css" href="gmaj.css">
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</head>
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<body>
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<p class=vvlarge>
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<h2>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</h2>
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<p class=vvlarge>
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Gmaj is a tool designed for viewing and manipulating Generalized
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Multiple Alignments (GMAs) produced by sequence-symmetric alignment
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programs such as <a href="http://www.bx.psu.edu/miller_lab/">TBA</a>
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(though it can also be used with MAF format alignments from other
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sources). It can display interactive graphical and text
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representations of the alignments, diagrams showing the locations
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of exons and repeats, and other annotations -- all with the user's
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choice of reference sequence.
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<p>
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The program is written in Java in order to provide a graphical
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user interface that is portable across a variety of computer
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platforms; indeed its name stands for "Generalized Multiple
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Alignments with Java". It requires <b>Java 1.3 or higher</b>,
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and for best compatibility
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<a href="http://java.com/en/download/manual.jsp">Sun's JRE</a>
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(or JDK) is recommended.
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<p>
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Gmaj can be run in two different modes: as a stand-alone
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application (for viewing local data files yourself) or as an
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applet over the world-wide web (to display your data on a server
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for viewing by others). These modes are mostly similar, but
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have a few minor differences due to the underlying capabilities
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of applets vs. applications in Java.
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<p>
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<blockquote class=notop>
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<a href="http://globin.bx.psu.edu/java/gmaj/demo.html"
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>Applet demo</a>
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</blockquote>
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<p class=large>
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The current Gmaj distribution package is available for download
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as a compressed zip archive,
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<code><a href="http://globin.bx.psu.edu/dist/gmaj/gmaj.zip"
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>gmaj.zip</a></code>.
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<p>
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The following additional documentation files are included:
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<ul>
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<li> <a href="gmaj_news.html">What's New in Gmaj</a><br>
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A summary of the changes in each released version of Gmaj.
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(Note important <b>bug fix</b> on 2005-Sep-13.)
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<p>
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<li> <a href="gmaj_bugs.html">Known Bugs in Gmaj</a><br>
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A discussion of the known bugs and anomalies we have
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observed, but not yet resolved. Some of these may depend
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on your computer platform and/or version of Java.
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<p>
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<li> <a href="gmaj_install.html">Installing Gmaj</a><br>
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Describes how to unpack and set up Gmaj, for both
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stand-alone and applet use.
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<p>
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<li> <a href="gmaj_help.html">Starting and Running Gmaj</a><br>
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Describes how to start Gmaj and use the GUI, in both
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stand-alone and applet modes. This is the file that Gmaj's
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"Help - Manual" menu item points to.
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<p>
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<li> <a href="gmaj_input.html">Input Files for Gmaj</a><br>
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Detailed descriptions of the input files used by Gmaj, and
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their formats.
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<p>
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<li> <code><a href="sample.gmaj">sample.gmaj</a></code><br>
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A sample template for the parameters file that tells Gmaj
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which data files to load, among other things. Includes
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explanatory comments at the bottom. This file is optional
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if you don't want to display any annotations or use the
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other features it provides.
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</ul>
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<p>
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<p class=vvlarge>
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<hr>
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<i>Cathy Riemer, June 2008</i>
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</body>
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</html>
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