/static/gmaj/docs/gmaj_readme.html

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  5. <title>Gmaj: an Interactive Viewer for Multiple Sequence Alignments</title>
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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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  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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