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| 3 | <html> |
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| 4 | <head> |
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| 5 | <title>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</title> |
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| 6 | <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> |
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| 7 | <meta http-equiv="Content-Style-Type" content="text/css"> |
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| 8 | <link rel="stylesheet" type="text/css" href="gmaj.css"> |
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| 9 | </head> |
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| 10 | <body> |
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| 11 | <p class=vvlarge> |
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| 12 | <h2>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</h2> |
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| 13 | <p class=vvlarge> |
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| 14 | Gmaj is a tool designed for viewing and manipulating Generalized |
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| 15 | Multiple Alignments (GMAs) produced by sequence-symmetric alignment |
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| 16 | programs such as <a href="http://www.bx.psu.edu/miller_lab/">TBA</a> |
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| 17 | (though it can also be used with MAF format alignments from other |
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| 18 | sources). It can display interactive graphical and text |
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| 19 | representations of the alignments, diagrams showing the locations |
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| 20 | of exons and repeats, and other annotations -- all with the user's |
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| 21 | choice of reference sequence. |
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| 22 | <p> |
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| 23 | The program is written in Java in order to provide a graphical |
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| 24 | user interface that is portable across a variety of computer |
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| 25 | platforms; indeed its name stands for "Generalized Multiple |
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| 26 | Alignments with Java". It requires <b>Java 1.3 or higher</b>, |
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| 27 | and for best compatibility |
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| 28 | <a href="http://java.com/en/download/manual.jsp">Sun's JRE</a> |
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| 29 | (or JDK) is recommended. |
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| 30 | <p> |
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| 31 | Gmaj can be run in two different modes: as a stand-alone |
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| 32 | application (for viewing local data files yourself) or as an |
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| 33 | applet over the world-wide web (to display your data on a server |
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| 34 | for viewing by others). These modes are mostly similar, but |
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| 35 | have a few minor differences due to the underlying capabilities |
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| 36 | of applets vs. applications in Java. |
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| 37 | <p> |
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| 38 | <blockquote class=notop> |
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| 39 | <a href="http://globin.bx.psu.edu/java/gmaj/demo.html" |
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| 40 | >Applet demo</a> |
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| 41 | </blockquote> |
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| 42 | <p class=large> |
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| 43 | The current Gmaj distribution package is available for download |
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| 44 | as a compressed zip archive, |
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| 45 | <code><a href="http://globin.bx.psu.edu/dist/gmaj/gmaj.zip" |
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| 46 | >gmaj.zip</a></code>. |
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| 47 | <p> |
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| 48 | The following additional documentation files are included: |
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| 49 | <ul> |
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| 50 | <li> <a href="gmaj_news.html">What's New in Gmaj</a><br> |
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| 51 | A summary of the changes in each released version of Gmaj. |
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| 52 | (Note important <b>bug fix</b> on 2005-Sep-13.) |
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| 53 | <p> |
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| 54 | <li> <a href="gmaj_bugs.html">Known Bugs in Gmaj</a><br> |
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| 55 | A discussion of the known bugs and anomalies we have |
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| 56 | observed, but not yet resolved. Some of these may depend |
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| 57 | on your computer platform and/or version of Java. |
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| 58 | <p> |
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| 59 | <li> <a href="gmaj_install.html">Installing Gmaj</a><br> |
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| 60 | Describes how to unpack and set up Gmaj, for both |
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| 61 | stand-alone and applet use. |
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| 62 | <p> |
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| 63 | <li> <a href="gmaj_help.html">Starting and Running Gmaj</a><br> |
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| 64 | Describes how to start Gmaj and use the GUI, in both |
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| 65 | stand-alone and applet modes. This is the file that Gmaj's |
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| 66 | "Help - Manual" menu item points to. |
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| 67 | <p> |
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| 68 | <li> <a href="gmaj_input.html">Input Files for Gmaj</a><br> |
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| 69 | Detailed descriptions of the input files used by Gmaj, and |
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| 70 | their formats. |
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| 71 | <p> |
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| 72 | <li> <code><a href="sample.gmaj">sample.gmaj</a></code><br> |
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| 73 | A sample template for the parameters file that tells Gmaj |
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| 74 | which data files to load, among other things. Includes |
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| 75 | explanatory comments at the bottom. This file is optional |
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| 76 | if you don't want to display any annotations or use the |
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| 77 | other features it provides. |
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| 78 | </ul> |
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| 79 | <p> |
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| 80 | |
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| 81 | <p class=vvlarge> |
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| 82 | <hr> |
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| 83 | <i>Cathy Riemer, June 2008</i> |
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| 84 | </body> |
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| 85 | </html> |
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