+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html>\r
-<head>\r
-<!-- TemplateBeginEditable name="doctitle" --> \r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- TemplateEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- TemplateBeginEditable name="head" --><!-- TemplateEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: Geneva, Arial, Helvetica, sans-serif;\r
- font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
- <table border="0">\r
- <tr> \r
- <td width="700" ><center>\r
- <table width="550" border="0">\r
- <tr>\r
- <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../snap22med.gif" width="291" height="116" border="0" align="absmiddle"></a></div></td>\r
- <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
- </font></strong></font> </div>\r
- <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
- multiple alignment editor</font> </div></td>\r
- </tr>\r
- </table>\r
- </center></td>\r
- </tr>\r
- </table>\r
- <br>\r
- <table border="0">\r
- <tr> \r
- <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
- <ul>\r
- <li><a href="../version2/index.html">Jalview</a></li>\r
- </ul>\r
- <strong>Examples</strong> <ul>\r
- <li><a href="../version2/examples/applets.html">Applet</a></li>\r
- <li><a href="../version2/examples/examples.html">Application</a></li>\r
- </ul>\r
- <strong>Reference</strong> <ul>\r
- <li> <a href="../jalview.pdf" target="_blank">"The Jalview Java<br>\r
- Alignment Editor,"<br>\r
- </a></li>\r
- <a href="../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
- </ul>\r
- <strong>Source Code</strong> <ul>\r
- <li>Jalview 2</li>\r
- </ul>\r
- <p><strong>Feedback</strong></p>\r
- <p> <img src="../help.gif" width="151" height="43"> </p>\r
- <p><br>\r
- <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../bbsrc.jpg"></a> \r
- </p></td>\r
- <td width="499" valign="top"><!-- TemplateBeginEditable name="Contents" -->Contents<!-- TemplateEndEditable --> \r
- </td>\r
- </tr>\r
- </table>\r
-</div>\r
-</body>\r
-</html>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: Geneva, Arial, Helvetica, sans-serif;\r
- font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
- <table border="0">\r
- <tr> \r
- <td width="700" ><center>\r
- <table width="550" border="0">\r
- <tr>\r
- <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../../snap22med.gif" width="291" height="116" border="0" align="absmiddle"></a></div></td>\r
- <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
- </font></strong></font> </div>\r
- <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
- multiple alignment editor</font> </div></td>\r
- </tr>\r
- </table>\r
- </center></td>\r
- </tr>\r
- </table>\r
- <br>\r
- <table border="0">\r
- <tr> \r
- <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
- <ul>\r
- <li><a href="../index.html">Jalview</a></li>\r
- </ul>\r
- <strong>Examples</strong> <ul>\r
- <li><a href="applets.html">Applet</a></li>\r
- <li><a href="examples.html">Application</a></li>\r
- </ul>\r
- <strong>Reference</strong> <ul>\r
- <li> <a href="../../jalview.pdf" target="_blank">"The Jalview Java<br>\r
- Alignment Editor,"<br>\r
- </a></li>\r
- <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
- </ul>\r
- <strong>Source Code</strong> <ul>\r
- <li>Jalview 2</li>\r
- </ul>\r
- <p><strong>Feedback</strong></p>\r
- <p> <img src="../../help.gif" width="151" height="43"> </p>\r
- <p><br>\r
- <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
- </p></td>\r
- <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" -->\r
- <p>Jalview2 comes in two distinct flavours.<br>\r
- <br>\r
- The main application allows connection to multiple web services provided\r
- at the University of Dundee as well as a host of additional useful features\r
- such as printing, making images from your alignment and annotating your\r
- alignment. <br>\r
- You need to download and install this software.</p>\r
- <p> Pressing one of the buttons below will load up a cut down version\r
- of Jalview2 multiple alignment editor, which runs within your web browser.</p>\r
- <H4>Alignment 1 - Serine proteases (6 sequences x 279 residues)</H4>\r
- <center>\r
-\r
- <applet code="jalview.bin.JalviewLite"\r
- archive="jalviewlite.jar"\r
- width="200" height="40">\r
- <param name="file" value="serprot.msf">\r
- </applet>\r
-\r
- </center>\r
- <H4>Alignment 2 - Lipases (16 sequences x 487 residues)</H4>\r
- <center>\r
- <applet code="jalview.bin.JalviewLite"\r
- archive="jalviewlite.jar"\r
- width="200" height="40">\r
- <param name="file" value="lipase.msf">\r
- <param name="defaultColour" value="Clustal">\r
- <param name="showFullId" value="false">\r
- </applet></center>\r
- <H4>Alignment 3 - Glutathione S-transferases (61 sequences x 290 residues) With associated tree</H4>\r
- <center>\r
- <applet code="jalview.bin.JalviewLite"\r
- archive="jalviewlite.jar"\r
- width="200" height="40">\r
- <param name="file" value="glut.msf">\r
- <param name="defaultColour" value="Strand Propensity">\r
- <param name="showConsensus" value="false">\r
- <param name="showConservation" value="false">\r
- <param name="treeFile" value="glut.newick">\r
- </applet>\r
- </center>\r
- <p>The applet takes the following Parameters:</p>\r
- <table width="325" border="1" align="center" >\r
- <tr>\r
- <td width="103"><strong>name</strong></td>\r
- <td width="190"><strong>value</strong></td>\r
- </tr>\r
- <tr>\r
- <td>file</td>\r
- <td><em>fileName</em></td>\r
- </tr>\r
- <tr>\r
- <td>showFullId</td>\r
- <td>true false</td>\r
- </tr>\r
- <tr>\r
- <td>showAnnotation</td>\r
- <td>true false</td>\r
- </tr>\r
- <tr>\r
- <td>showConservation</td>\r
- <td>true false</td>\r
- </tr>\r
- <tr>\r
- <td>showQuality</td>\r
- <td>true false</td>\r
- </tr>\r
- <tr>\r
- <td>showConsensus</td>\r
- <td>true false</td>\r
- </tr>\r
- <tr>\r
- <td>defaultColour</td>\r
- <td>Clustal, Blosum62, % Identity, Zappo, Hydrophobic, Helix Propensity,\r
- Strand Propensity, Turn Propensity, Buried Index, Nucleotide</td>\r
- </tr>\r
- </table>\r
- <p align="center"> </p>\r
- <!-- InstanceEndEditable --> \r
- </td>\r
- </tr>\r
- </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: Geneva, Arial, Helvetica, sans-serif;\r
- font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
- <table border="0">\r
- <tr> \r
- <td width="700" ><center>\r
- <table width="550" border="0">\r
- <tr>\r
- <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../../snap22med.gif" width="291" height="116" border="0" align="absmiddle"></a></div></td>\r
- <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
- </font></strong></font> </div>\r
- <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
- multiple alignment editor</font> </div></td>\r
- </tr>\r
- </table>\r
- </center></td>\r
- </tr>\r
- </table>\r
- <br>\r
- <table border="0">\r
- <tr> \r
- <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
- <ul>\r
- <li><a href="../index.html">Jalview</a></li>\r
- </ul>\r
- <strong>Examples</strong> <ul>\r
- <li><a href="applets.html">Applet</a></li>\r
- <li><a href="examples.html">Application</a></li>\r
- </ul>\r
- <strong>Reference</strong> <ul>\r
- <li> <a href="../../jalview.pdf" target="_blank">"The Jalview Java<br>\r
- Alignment Editor,"<br>\r
- </a></li>\r
- <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
- </ul>\r
- <strong>Source Code</strong> <ul>\r
- <li>Jalview 2</li>\r
- </ul>\r
- <p><strong>Feedback</strong></p>\r
- <p> <img src="../../help.gif" width="151" height="43"> </p>\r
- <p><br>\r
- <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
- </p></td>\r
- <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
- <p>Many alignment tools which require time consuming and/or large proccessing \r
- power are currently being developed as Web Services within the Barton \r
- Group, Dundee, and added to the Jalview interface.</p>\r
- <p> </p>\r
- <center><img src="jpredQ.jpg" width="519" height="252">\r
- <table width="100" border="1" cellspacing="5" cellpadding="5">\r
- <tr>\r
- <td><img src="jpred.jpg" width="451" height="257"></td>\r
- </tr>\r
- </table>\r
- </center>\r
- <p align="center"> </p>\r
- <p align="center"> </p>\r
- <p align="center"><a href="examples2.html"><strong><font size="3">Next \r
- ></font></strong></a></p>\r
- <!-- InstanceEndEditable --> \r
- </td>\r
- </tr>\r
- </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: Geneva, Arial, Helvetica, sans-serif;\r
- font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
- <table border="0">\r
- <tr> \r
- <td width="700" ><center>\r
- <table width="550" border="0">\r
- <tr>\r
- <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../../snap22med.gif" width="291" height="116" border="0" align="absmiddle"></a></div></td>\r
- <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
- </font></strong></font> </div>\r
- <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
- multiple alignment editor</font> </div></td>\r
- </tr>\r
- </table>\r
- </center></td>\r
- </tr>\r
- </table>\r
- <br>\r
- <table border="0">\r
- <tr> \r
- <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
- <ul>\r
- <li><a href="../index.html">Jalview</a></li>\r
- </ul>\r
- <strong>Examples</strong> <ul>\r
- <li><a href="applets.html">Applet</a></li>\r
- <li><a href="examples.html">Application</a></li>\r
- </ul>\r
- <strong>Reference</strong> <ul>\r
- <li> <a href="../../jalview.pdf" target="_blank">"The Jalview Java<br>\r
- Alignment Editor,"<br>\r
- </a></li>\r
- <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
- </ul>\r
- <strong>Source Code</strong> <ul>\r
- <li>Jalview 2</li>\r
- </ul>\r
- <p><strong>Feedback</strong></p>\r
- <p> <img src="../../help.gif" width="151" height="43"> </p>\r
- <p><br>\r
- <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
- </p></td>\r
- <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" -->\r
- <p>Several of the most popular sequence alignment algorithms and / or \r
- programs have been implemented as web services which Jalview has access \r
- to.</p>\r
- <p>The figure below shows the web service status window indicating that \r
- a Muscle Alignment job as run to completion. The window shows important \r
- feedback regarding the alignement. </p>\r
- <p><img src="muscle.jpg" width="518" height="377"> </p>\r
- <p align="center"> </p>\r
- <p align="center"><strong><font size="3"><a href="examples.html">< \r
- Back</a> <a href="examples3.html">Next ></a></font></strong></p>\r
- <!-- InstanceEndEditable --> \r
- </td>\r
- </tr>\r
- </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: Geneva, Arial, Helvetica, sans-serif;\r
- font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
- <table border="0">\r
- <tr> \r
- <td width="700" ><center>\r
- <table width="550" border="0">\r
- <tr>\r
- <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../../snap22med.gif" width="291" height="116" border="0" align="absmiddle"></a></div></td>\r
- <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
- </font></strong></font> </div>\r
- <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
- multiple alignment editor</font> </div></td>\r
- </tr>\r
- </table>\r
- </center></td>\r
- </tr>\r
- </table>\r
- <br>\r
- <table border="0">\r
- <tr> \r
- <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
- <ul>\r
- <li><a href="../index.html">Jalview</a></li>\r
- </ul>\r
- <strong>Examples</strong> <ul>\r
- <li><a href="applets.html">Applet</a></li>\r
- <li><a href="examples.html">Application</a></li>\r
- </ul>\r
- <strong>Reference</strong> <ul>\r
- <li> <a href="../../jalview.pdf" target="_blank">"The Jalview Java<br>\r
- Alignment Editor,"<br>\r
- </a></li>\r
- <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
- </ul>\r
- <strong>Source Code</strong> <ul>\r
- <li>Jalview 2</li>\r
- </ul>\r
- <p><strong>Feedback</strong></p>\r
- <p> <img src="../../help.gif" width="151" height="43"> </p>\r
- <p><br>\r
- <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
- </p></td>\r
- <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
- <p align="center">Jalview will search Uniprot to find the exact protein \r
- sequence match from any input alignment file. This can be used to display \r
- sequence features, moving the mouse over the displayed feature will \r
- reveal more information. </p>\r
- <p align="center"><img src="uniprot.gif" width="516" height="252"></p>\r
- <p align="center"><br>\r
- Jalview allows the alignment to be "wrapped"</p>\r
- <p align="center"><img src="wrap.gif" width="494" height="386"></p>\r
- <p align="center"><strong><font size="3"><a href="examples2.html">< \r
- Back</a> <a href="examples4.html">Next ></a></font></strong></p>\r
- <!-- InstanceEndEditable --> \r
- </td>\r
- </tr>\r
- </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: Geneva, Arial, Helvetica, sans-serif;\r
- font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
- <table border="0">\r
- <tr> \r
- <td width="700" ><center>\r
- <table width="550" border="0">\r
- <tr>\r
- <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../../snap22med.gif" width="291" height="116" border="0" align="absmiddle"></a></div></td>\r
- <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
- </font></strong></font> </div>\r
- <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
- multiple alignment editor</font> </div></td>\r
- </tr>\r
- </table>\r
- </center></td>\r
- </tr>\r
- </table>\r
- <br>\r
- <table border="0">\r
- <tr> \r
- <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
- <ul>\r
- <li><a href="../index.html">Jalview</a></li>\r
- </ul>\r
- <strong>Examples</strong> <ul>\r
- <li><a href="applets.html">Applet</a></li>\r
- <li><a href="examples.html">Application</a></li>\r
- </ul>\r
- <strong>Reference</strong> <ul>\r
- <li> <a href="../../jalview.pdf" target="_blank">"The Jalview Java<br>\r
- Alignment Editor,"<br>\r
- </a></li>\r
- <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
- </ul>\r
- <strong>Source Code</strong> <ul>\r
- <li>Jalview 2</li>\r
- </ul>\r
- <p><strong>Feedback</strong></p>\r
- <p> <img src="../../help.gif" width="151" height="43"> </p>\r
- <p><br>\r
- <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
- </p></td>\r
- <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
- Many new features have been added to the Jalview interface, \r
- such as the Overview window which aids navigation around the whole alignment.\r
- <p align="center"><img src="overview.gif" width="544" height="185"></p>\r
- <p align="center"><br>\r
- Search using regular expressions.</p>\r
- <p align="center"><img src="search.gif" width="429" height="223"></p>\r
- The functionality of the original Jalview has been maintained \r
- and enhanced in the new interface. Below is an example of an average \r
- distance tree, calculated from the input alignment, being used to cluster \r
- sequences in the main alignment window.<br>\r
- The user has then applied "Conservation Colouring" to the \r
- alignment, the result of which shows conservation within the clustered \r
- sequences. <img src="tree.gif" width="696" height="360">\r
- <p align="center"><font size="3"><strong><a href="examples3.html">< \r
- Back</a></strong></font> <strong><a href="examples5.html"><font size="3"> Next \r
- ></font></a></strong></p>\r
- <!-- InstanceEndEditable --> \r
- </td>\r
- </tr>\r
- </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" --> \r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable --> \r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: Geneva, Arial, Helvetica, sans-serif;\r
- font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
- <table border="0">\r
- <tr> \r
- <td width="700" ><center>\r
- <table width="550" border="0">\r
- <tr>\r
- <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../../snap22med.gif" width="291" height="116" border="0" align="absmiddle"></a></div></td>\r
- <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview \r
- </font></strong></font> </div>\r
- <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a \r
- multiple alignment editor</font> </div></td>\r
- </tr>\r
- </table>\r
- </center></td>\r
- </tr>\r
- </table>\r
- <br>\r
- <table border="0">\r
- <tr> \r
- <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
- <ul>\r
- <li><a href="../index.html">Jalview</a></li>\r
- </ul>\r
- <strong>Examples</strong> <ul>\r
- <li><a href="applets.html">Applet</a></li>\r
- <li><a href="examples.html">Application</a></li>\r
- </ul>\r
- <strong>Reference</strong> <ul>\r
- <li> <a href="../../jalview.pdf" target="_blank">"The Jalview Java<br>\r
- Alignment Editor,"<br>\r
- </a></li>\r
- <a href="../../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a> \r
- </ul>\r
- <strong>Source Code</strong> <ul>\r
- <li>Jalview 2</li>\r
- </ul>\r
- <p><strong>Feedback</strong></p>\r
- <p> <img src="../../help.gif" width="151" height="43"> </p>\r
- <p><br>\r
- <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../../bbsrc.jpg"></a> \r
- </p></td>\r
- <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" --> \r
- <p align="center">Jalview maintains the ability to perform Principal Component \r
- Analysis on an alignment. The method is used to cluster similar sequences, \r
- the user may then select sequences from this 3D visual display.</p>\r
- <p align="center"><img src="pca.gif" width="394" height="396"></p>\r
- <p align="center"><br>\r
- PDB structures may be displayed if Jalview can find a match of the input \r
- sequence and Uniprot. </p>\r
- <p align="center"><img src="pdb.gif" width="395" height="397"></p>\r
- <p align="center"><strong><a href="examples4.html"><font size="3">< \r
- Back</font></a></strong></p>\r
- <!-- InstanceEndEditable --> \r
- </td>\r
- </tr>\r
- </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
+++ /dev/null
-PileUp\r
-\r
-\r
-\r
- MSF: 439 Type: P Check: 2277 .. \r
-\r
- Name: AJPMQA oo Len: 439 Check: 4128 Weight: 1.00\r
- Name: AJFBQA oo Len: 439 Check: 6903 Weight: 1.00\r
- Name: AJAAQ oo Len: 439 Check: 4168 Weight: 1.00\r
- Name: AJFBQB oo Len: 439 Check: 5921 Weight: 1.00\r
- Name: AJPMQ1 oo Len: 439 Check: 4951 Weight: 1.00\r
- Name: AJFBQ oo Len: 439 Check: 7754 Weight: 1.00\r
- Name: AJYLNB oo Len: 439 Check: 1096 Weight: 1.00\r
- Name: AJRZQG oo Len: 439 Check: 7565 Weight: 1.00\r
- Name: AJLCQB oo Len: 439 Check: 5610 Weight: 1.00\r
- Name: AJRZQB oo Len: 439 Check: 5547 Weight: 1.00\r
- Name: AJFBQD oo Len: 439 Check: 2775 Weight: 1.00\r
- Name: AJPMQ2 oo Len: 439 Check: 3516 Weight: 1.00\r
- Name: AJRZQD oo Len: 439 Check: 1469 Weight: 1.00\r
- Name: AJBHQ oo Len: 439 Check: 2409 Weight: 1.00\r
- Name: AJDHQ oo Len: 439 Check: 5591 Weight: 1.00\r
- Name: AJMSQ oo Len: 439 Check: 9358 Weight: 1.00\r
- Name: AJMSQ3 oo Len: 439 Check: 166 Weight: 1.00\r
- Name: AJHYQ oo Len: 439 Check: 415 Weight: 1.00\r
- Name: AJRTQ oo Len: 439 Check: 9855 Weight: 1.00\r
- Name: AJHUQ oo Len: 439 Check: 1969 Weight: 1.00\r
- Name: AJCHQ oo Len: 439 Check: 7657 Weight: 1.00\r
- Name: AJFF2C oo Len: 439 Check: 4626 Weight: 1.00\r
- Name: AJFF1M oo Len: 439 Check: 6582 Weight: 1.00\r
- Name: AJSM2V oo Len: 439 Check: 8742 Weight: 1.00\r
- Name: AJSM2H oo Len: 439 Check: 4241 Weight: 1.00\r
- Name: AJKXQ oo Len: 439 Check: 5092 Weight: 1.00\r
- Name: AJZJQ2 oo Len: 439 Check: 4171 Weight: 1.00\r
-\r
-//\r
-\r
-\r
-\r
-AJPMQA .......... .......... .......... .......... .......... \r
-AJFBQA .......... .......... .......... .......... .......... \r
-AJAAQ .......... .......... .......... .......... .......... \r
-AJFBQB .......... .......... .......... .......... .......... \r
-AJPMQ1 .......... .......... .......... .......... .......... \r
-AJFBQ .......... .......... .......... .......... .......... \r
-AJYLNB .......... .......... .......... .......... .......... \r
-AJRZQG .......... .......... .......... .......... .......... \r
-AJLCQB .......... .......... .......... .......... .......... \r
-AJRZQB .......... .......... .......... .......... .......... \r
-AJFBQD ........MA QILAPSTQWQ MRFTKSSRHA SPITSNTWSS LLMKQNKK.T \r
-AJPMQ2 ........MA QILAPSTQWQ MRITKTSPCA TPITSKMWSS LVMKQTKKVA \r
-AJRZQD ......MAQA VVPAMQCQVG AVR....ARP AAAAAAAGGR VWGVRRTGRG \r
-AJBHQ ....MQVRRD DDGAGGCAGD AVPGGGEGQD GVPARQPAGR VWGVSRAARA \r
-AJDHQ .......... .......... .......... .......... .......... \r
-AJMSQ .......... .......... .......... .......... .......... \r
-AJMSQ3 .......... .......... .......... .......... .......... \r
-AJHYQ .......... .......... .......... .......... .......... \r
-AJRTQ .......... .......... .......... .......... .......... \r
-AJHUQ .......... .......... .......... .......... .......... \r
-AJCHQ .......... .......... .......... .......... .......... \r
-AJFF2C .......... .......... .......... .......... .......... \r
-AJFF1M .......... .......... ...MALRVAG LFLKKELVAP ATQQLRLLRT \r
-AJSM2V .......... .......... .......... .......... .......... \r
-AJSM2H .......... .......... .......... .......... .......... \r
-AJKXQ .......... .......... .......... .......... .......... \r
-AJZJQ2 .......... .......... .......... .......... .......... \r
-\r
-\r
-AJPMQA .......... ....MSSLSD LINFNLSDST EKIIAEYIWV GGS..GIDIR \r
-AJFBQA .......... ....MSLLSD LINLNLSEST EKIIAEYIWV GGS..GMDLR \r
-AJAAQ .......... ....MSLLSD LINLDLSETT EKIIAEYIWI GGS..GLDLR \r
-AJFBQB .......... ....MSLLSD LINLNLSDTT EKVIAEYIWI GGS..GLDLR \r
-AJPMQ1 .......... .....MSLSD LINLDLSGTT EKIIAEYIWI GGS..GLDLR \r
-AJFBQ .......... ....MSSISD LVNLNLSDST ERVIAEYIWV GGS..GMDMR \r
-AJYLNB .......... ....MSLLSD LINLNLSDTT EKIIAEYIWV GGS..GVDLR \r
-AJRZQG .......... ....MASLTD LVNLNLSDTT EKIIAEYIWI GGS..GMDLR \r
-AJLCQB .......... ....MALLSD LVNLDLSSIN DKIIAEYIWI GGS..GMDLR \r
-AJRZQB .......... ....MANLTD LVNLNLSDCS DKIIAEYIWV GGS..GIDLR \r
-AJFBQD SSFRVLAVKS DGSTINRLEG LLNLDITPFT DKIIAEYIWI GGT..GIDVR \r
-AJPMQ2 HSFRVMAVNS ENGTINRVED LLNLDITPFT DSIIAEYIWI GGT..GIDVR \r
-AJRZQD TSRVMAVSTE TTGVVTRMEQ LLNMDTTPFT DKIIAEYIWV GGT..GIDLR \r
-AJBHQ TSKVLALGPE TTGVIQRMQQ LLDMDTTPFT DKIIAEYIWV GGS..GIDLR \r
-AJDHQ .......... .......... .......... .......... .......... \r
-AJMSQ ......MATS ASSHLNKGIK QMYMSLPQGE .KVQAMYIWV DGT..GEGLR \r
-AJMSQ3 ......MATS ASSHVNKGIK QMYMSLPQGE .KIQAMYIWV NGT..GEPLR \r
-AJHYQ ......MATS ASSHLNKNIK QMYLCLPQGE .KVQAMYIWV DGT..GEGLR \r
-AJRTQ ......MATS ASSHLNKGIK QMYMNLPQGE .KIQLMYIWV DGT..GEGLR \r
-AJHUQ ......MTTS ASSHLNKGIK QVYMSLPQGE .KVQAMYIWI DGT..GEGLR \r
-AJCHQ ......MATS ASSHLSKAIK HMYMKLPQGE .KVQAMYIWI DGT..GEHLR \r
-AJFF2C ..SARILEDS PNARINKTIL DRYLSLPLQE NIVQATYVWI DGT..GEDLR \r
-AJFF1M GNRSQFLANS PNTALDKSIL QRYRNLETPA NRVQATYLWI DGT..GENIR \r
-AJSM2V .......... .......... .......... MTFKAEYIWI DGTEPTAKLR \r
-AJSM2H .......... .......... .......... MSIKAEYIWI DGTQPTAKLR \r
-AJKXQ .......... .......... .......... MSYQAEYIWI DGTEPEPLMR \r
-AJZJQ2 .......... .......... .........M TKYKLEYIWL DGYTPTPNLR \r
-\r
-\r
-AJPMQA AR.TLPGPVS DPAKLPKWNY DGSSTNQAPG KDSEVILYPQ AIFKDPFR.N \r
-AJFBQA AR.TLPGPVD DPAKLPKWNY DGSSTDQAPG DDSEVILYPQ AIFKDPFR.N \r
-AJAAQ AR.TLPGPVT DPSQLPKWNY DGSSTGQAPG EDSEVIIYPQ AIFKDPFR.N \r
-AJFBQB AR.TLPGPVK NPSELPKWNY DGSSTGQAPG QDSEVIIYPQ AIFKDPFR.N \r
-AJPMQ1 AR.TLPGPVT DPSELPKWNY DGSSTGQAPG QDSEVILYPQ AIFKDPFR.N \r
-AJFBQ AR.TLSGPVK DPSKLPKWNY DGSSTGQAPG QDSEVILYPQ TIFRDPFR.N \r
-AJYLNB AR.TLSGPVN DPSKLPKWNY DGSSTGQAPG KDSEVILWPQ AIFKDPFR.N \r
-AJRZQG AR.TLSGPVT DPSKLPKWNY DGQAPGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJLCQB AR.TISRPVS .DPSELPKWN YDGSSTGQAP GEDSEVIIYP QAIFKDPFKN \r
-AJRZQB AR.TVKGPIT DVSQLPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.D \r
-AJFBQD SR.TISKPVE HPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJPMQ2 SR.TISKPVS HPSEVPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJRZQD SR.TISKPVE DPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJBHQ SR.TISKPVE DPSELPKWNY DGSSTGQAPG EDSEVILYPQ AIFKDPFR.N \r
-AJDHQ .......... .......... .......... .......... .......... \r
-AJMSQ TR.TLDCEPK CVEELPEWNF DGSSTFQSEG SNSDMYLHPV AMFRDPFR.P \r
-AJMSQ3 TCRTLDCEPK CVEELPEWNF DGSSTFQSEG SNSNMYLHPV AMFRDPFR.. \r
-AJHYQ TR.TLDCEPK CVEELPEWNF DGSSTFQSEG SNSDMYLSPV AMFRDPFR.P \r
-AJRTQ TR.TLDCDPK CVEELPEWNF DGSSTFQSEG SNSDMYLHPV AMFRDPFR.P \r
-AJHUQ TR.TLDSEPK CVEELPEWNF DGSSTLQSEG SNSDMYLVPA AMFRDPFR.P \r
-AJCHQ TR.TLDHEPK SLEDLPEWNF DGSSTFQAEG SNSDMYLRPA AMFRDPFR.P \r
-AJFF2C DR.TLDFIPQ SPKELPVWNY DGSSCYQAEG SNSDTYLYPV AIYKDPFR.N \r
-AJFF1M DR.VLDKVPS SVEDLPDWQY DGSSTYQAHG ENSDTTLKPR AIYRDPFKKN \r
-AJSM2V TKIITGQPAG .LDALPIWGF DGSSTNQAEG HSSDCVLKPV FTCPDPIRGD \r
-AJSM2H TKILSDGSR. ....LPRWGF DGSSTNQAEG HASDLVLEPV FSCPDPIRGD \r
-AJKXQ TRIIKDGKE. ....PEIWGF DGSSTNQAPG SNSDCVLRPV FETPDPIRGD \r
-AJZJQ2 TQIKEFASFP TLEHVPLWGF DGSSTQQAEG HSSDCVLKPV AVFPDAARTN \r
-\r
-\r
-AJPMQA NILVICDVYT PAGEP.LPTN KRYNAAKIFS HPDVAAEVPW YGIEQELLQK \r
-AJFBQA NILVICDVYT PAGEP.LPTN KRYDAAKIFS HPDVVAEVPW YGIEQELLQK \r
-AJAAQ NILVMCDAYT PAGEP.IPTN KRHAAAKIFS HPDVVAEVPW YGIEQELLQK \r
-AJFBQB NILVICDAYT PAGEP.IPTN KRHNAAKIFS NPDVVAEEPW YGIEQELLQK \r
-AJPMQ1 HILVMCDAYS PAGEP.IPTN KRHAAAKVFS HPDVVAEETW YGIEQELLQK \r
-AJFBQ NILVMCDAYT PAGEP.IPTN KRHNAAKIFS NPEVVAEEPW YGIEQELLQK \r
-AJYLNB NILVICDTYT PSGKP.IPTN KRHAAAKIFS HPDVAAEEPW FGIEQELLQK \r
-AJRZQG NILVMCDCYT PAGEP.IPTN KRHNAAKIFS SPEVASEEPW YGIEQELLQK \r
-AJLCQB HILVMCDAYT PAGEP.IPTN KRAAAAKIFS NPEVEKEVTW YGIEQELLQK \r
-AJRZQB NILVMCDCYT PQGEP.IPTN KRHSAAKIFS HPDVVAEVPW YGIEQELLQK \r
-AJFBQD NILVICDAYT PAGEP.IPTN KRHRAAEVFS NPRVIAEVPW FGIEQELLQT \r
-AJPMQ2 NILVVCDAYT PAGEP.IPTN KRHRAAEIFS NPKVEAEIPW YGIEQELLQT \r
-AJRZQD NILVMCDTYT PAGEP.IPTN KRNRAAQVFS DPKVVSQVPW FGIEQELLQR \r
-AJBHQ NILVICDTYT PQGEP.IPTN KRHMAAQIFS DPKVTSQVQW FGIEQELMQR \r
-AJDHQ .......... .......... .......... ....KAQEPW FGIEQELLNS \r
-AJMSQ NKLVLCEVFK YNRKP.AETN LRH..ICKRI MDMVSNQHPW FGMEQELMGT \r
-AJMSQ3 NKLVLCEVFK YNRKP.AETN LRH..ICKRI MDMVSNQHPW FGMEQELMGT \r
-AJHYQ NKLVFCEVFK YNRKP.AETN LRH..SCKRI MDMVSNQHPW FGMEQELMGT \r
-AJRTQ NKLVFCEVFK YNRKP.AETN LRH..SCKRI MDMVSSQHPW FGMEQELMGT \r
-AJHUQ NKLVLCEVFK YNRRP.AETN LRH..TCKRI MDMVSNQHPW FGMEQELMGT \r
-AJCHQ NKLVLCEVFK YNRQS.ADTN LRH..TCRRI MDMVSNQHPW FGMEQELLGT \r
-AJFF2C NILVMCDTYK FDGTP.TDTN KRK..TCLEV ANKCAAEEPW FGIEQESDFD \r
-AJFF1M DVIVLCDTYS ADGKP.TASN KRA..AFQAA IDLISDQEPW FGIEQELLRR \r
-AJSM2V DILVLCEVLN IDLTPH.ASN TRAALAEVAE RFAA..QEPI FGIEQEFFQD \r
-AJSM2H HLLVLCEVLH TDLTPH.PSN TRALLRPVAE RFAG..QEPI FGIEQEFLKG \r
-AJKXQ NRLVLCEVQL TDFTP..PTN TRAAALGVAE RYAD..MSPM FGIEQEFFKD \r
-AJZJQ2 GVLVMCEVMM PDGKTPHASN KRATILDDAG ........AW FGFEQEFYKD \r
-\r
-\r
-AJPMQA DINWPLGWPI GG..YPGKQG PYYCGIGADK AY..GRDIVD AHYKAFAGIN \r
-AJFBQA DVNWPLGWPL GG..YPGPQG PYYCGVGADK AY..GRDIVD AHYKAYAGIN \r
-AJAAQ DINWPLGWPV GG..FPGPQG PYYCGAGADK AF..GRDIVD SHYKAYAGIN \r
-AJFBQB EVNWPVGWPV GG..FPGPQG PYYCGVGADK AF..GRDIVD AHYKAYAGIN \r
-AJPMQ1 DINWPLGWPA GG..YPGPQG PYYCSVGADK AF..GRDVVE AHYKAFAGIN \r
-AJFBQ DVQWPVGWPL GG..FPGPQG PYYCGIGANK AF..GRDIVD SHYKAYAGIN \r
-AJYLNB DIHWPIGMAL GG..FPGPQG PYYCGTGAEK AF..GRDIVD SHYKAYAGIN \r
-AJRZQG DINWPLGWPV GG..FPGPQG PYYCGIGADK SF..GRDIVD SHYKAYAGIN \r
-AJLCQB DTNWPLGWPL GG..FPGPQG PYYCGIGADK AF..GRDIVH AHYKAYAGVN \r
-AJRZQB DVNWPLGWPV GG..FPGPQG PYYCAAGAEK AF..GRDIVD AHYKAYAGIN \r
-AJFBQD NVNWPLGWPV GG..YPGPQG PYYCSAGADK SF..GRDISD AHYKAFAGIN \r
-AJPMQ2 NVKWPLGWPV GG..YPGPQG PYYCAAGADK SF..GRDISD AHYKAYAGIN \r
-AJRZQD DVNWPLGWPV GG..YPGPQG PYYCAVGSDK SF..GRDISD AHYKAYAGIN \r
-AJBHQ DVNWPLGWPV GG..YPGPQG PYYCAVGSDK SF..GRDISD AHYKAYAGIE \r
-AJDHQ VTKWPLGWPK GG..YPAGQG PYYCSVGAGR SI..GRDIPE VHYRCHAGIQ \r
-AJMSQ DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK \r
-AJMSQ3 DG.HPFGWPF NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK \r
-AJHYQ DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK \r
-AJRTQ DG.HPFGWPS NG..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGIK \r
-AJHUQ DG.HPFGWPS NG..FPGPQG PYYCGVGADR AY..GRDIVE AHYRAYAGVK \r
-AJCHQ DG.HPFGWPS NC..FPGPQG PYYCGVGADK AY..GRDIVE AHYRAYAGVK \r
-AJFF2C G....HHWAG QEW.FPDP.G PYYCGVGANK SS..PR.HKD AHYAPYAGTQ \r
-AJFF1M GR.TSFGWPE NG..FPAPQG PYYCGVGADR VY..ARDLVE AHVVAYAGID \r
-AJSM2V GY..PLGFPK GG..FPAPQG GYYCGVGADE IF..GRDVVE AHLDNKAGLA \r
-AJSM2H DR..PLGFPE GGG.YPAPQA DYYCGVGADA IF..GREIVE KHLDLAAGLG \r
-AJKXQ GR..PYGWPE VG..YPAPQG PYYCGVGGSK MP..GRQIVE RHTQADAGLA \r
-AJZJQ2 GR..PLGFPT SG..YPAPQG PYYTGVGFSN VGDVARKIVE EHLDLAAGIN \r
-\r
-\r
-AJPMQA ISGINGEVMP GQWEFQVGPS VGISAGDEIW AARYILERIT EIAVVSFDPK \r
-AJFBQA ISGINGEVMP GQWEFQVGPS VGISAGDEVW AARYILERIT ELAVVSFDPK \r
-AJAAQ ISGINGEVMP GQWEFQVGPS VGISAGDEIW VARYILERIT EVAVLSFDPK \r
-AJFBQB ISGINGEVMP GQWEFQVGPA VGISAGDELW VARYILERIT EVAVLSFDPK \r
-AJPMQ1 ISGINGEVMP GQWEFQVGPS VGISAGDEIW VARYILERIT EVAVLTFDPK \r
-AJFBQ ISGINGEVMP GQWEFQVGPS VGISAADELW VARYILERIT EIAVLSFDPK \r
-AJYLNB ISGINAEVMP GQWEFQVGPS IGISAGDELW VARYILERIT EIAVLSLDPK \r
-AJRZQG ISGINGEVMP GQWEFQVGPS VGISAGDQVW VARYILERIT EIAVVSFDPK \r
-AJLCQB ISGINGEVMP GQWEFQVGPS VGIAAADQIW VARYILERIT EIYVVSFDPK \r
-AJRZQB ISGINGEVMP GQWEFQVGPS VGIAAADQVW VARYILERVT EVAVLSLDPK \r
-AJFBQD ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ASRYILERIT EQAVLSLDPK \r
-AJPMQ2 ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ASRYILERIT EQAVLTLDPK \r
-AJRZQD ISGTNGEVMP GQWEYQVGPS VGIEAGDHIW ISRYILERIT EQAVLTLDPK \r
-AJBHQ ISGTNGEVMP GQWEYQVGPS VGIDAGDHIW ASRYILERIT EQAVLTLDPK \r
-AJDHQ ISGVNGEVLP SQWEYQVGPV EGIAMGDQMW MSRYLMYRVA ELFEVTFDPK \r
-AJMSQ ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW IARFILHRVC EDFIATFDPK \r
-AJMSQ3 ITGTNAEVMP AQW....... .......... .......... .......... \r
-AJHYQ ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW VARFILHRVC EDFIATFDPK \r
-AJRTQ ITGTNAEVMP AQWEFQIGPC EGIRMGDHLW VARFILHRVC EDFIATFDPK \r
-AJHUQ IAGTNAEVMP AQWEFQIGPC EGISMGDHLW VARFILHRVC EDFIATFDPK \r
-AJCHQ IGGTNAEVMP AQWEFQVGPC EGIEMGDHLW IARFILHRVC EDFIVSFDPK \r
-AJFF2C GVPTNAEVMP AQWEFQVGPC EGISIGDDLW MARFLLHRIS EEFVSTLDPK \r
-AJFF1M FAGTNAEVMP AQWEFQIGPA G.IKACDDLW VSRYILQRIA EEYVVTFDPK \r
-AJSM2V ISGINAEVMP GQWEFQVGPV SPLEVSDHLW VARWLLYRTA EDFAATLDPK \r
-AJSM2H LSGINAEVMP GQWEFQVGAL PPLEVSDHMW VARWLLHRVA EEFTASLDAK \r
-AJKXQ IEGTNAEVMM GQWEFQIGVL PAPAIGDQIW LGRWLLHRIA EDYEVSFAAK \r
-AJZJQ2 HEGINAEVAK GQWEFQIFGK GSKKAADEMW MARYLMLRLT EKYDIEFHCK \r
-\r
-\r
-AJPMQA PIPG.DWNGA GAHANFSTKS MRENGGYEVI KKAIEKLGLR HHIAAYGE.. \r
-AJFBQA PIPG.DWNGA GAHSNYSTKS MREEGGYEVI KKAIEKLGLR HHIAAYGK.. \r
-AJAAQ PIKG.DWNGA GAHTNYSTKS MREDGGYEVI LKAIEKLGKK HHIAAYGE.. \r
-AJFBQB PIKG.DWNGA GAHTNYSTKT MRNDGGYEEI KSAIQKLGKR HHIAAYGE.. \r
-AJPMQ1 PIKG.DWNGA GAHTNYSTKS MREDGGYEII KKAIEKLGKR LHISAYGE.. \r
-AJFBQ PIQG.DWNGA GAHTNYSTKS MRNDGGYEVI KKAITKLEKR HHIAAYGE.. \r
-AJYLNB PIPG.DWNGA GAHTNYSTKS MRNDGGYEVI KQAIEKLEKR HHIAAYGE.. \r
-AJRZQG PIPG.DWNGA GAHTNYSTKS MRNDGGYEII KSAIEKLKLR HHISAYGE.. \r
-AJLCQB PIPG.DWNGA GAHTNYSTKT MREEGGYEVI KKAIEKLGLR HHIAAYGE.. \r
-AJRZQB PIPG.DWNGA GAHTNFSTKS MREPGGYEVI KKAIDKLALR HHIAAYGE.. \r
-AJFBQD PIEG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHISAYGE.. \r
-AJPMQ2 PIEG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHIEAYGE.. \r
-AJRZQD PIQG.DWNGA GCHTNYSTKS MREDGGFEVI KKAILNLSLR HHISAYGE.. \r
-AJBHQ PIQG.DWNGA GCHTNYSTLS MREDGGFDVI KKAILNLSLR HHIAAYGE.. \r
-AJDHQ PIPG.DWNGS GGHVNFSNRQ PESPPAGKQS RSSAKKLGKR HHIAAYGE.. \r
-AJMSQ PIPG.NWNVA GCHTNFSTKA MREENGLKCI EEAIDKLSKR HHIRAYDPKG \r
-AJMSQ3 .......... .......... .......... .......... .......... \r
-AJHYQ PIPG.NWNGA GCHTNFSTKA MREENGLKHI EEAIEKLSKR HHIRAYDPKG \r
-AJRTQ PIPG.NWNGA GCHTNFSTKA MREENGLRCI EEAIDKLSKR HHIRAYDPKG \r
-AJHUQ PIPG.NWNGA GCHTNFSTKA MREENGLKYI EEAIEKLSKR HHIRAYDPKG \r
-AJCHQ PIPG.NWNGA GCHTNFSTKN MREDGGLKHI EEAIEKLSKR HHIRAYDPKG \r
-AJFF2C PMPG.DWNGA GAHTNVSTNA MREDGGIRDI EKAVAKLSKC HHIRAYDPKQ \r
-AJFF1M PMEG.QWNGA GAHTNFSTKE MRADGGIKAI EEAIEKLSKR HHIKAYYPKE \r
-AJSM2V PVKG.DWNGA GAHTNFSTKA MRESYDAIIT AAESLGEGSK PHVKNYGA.. \r
-AJSM2H PAKG.DWNGA GAHTNFSTRA MREGYDPIIT ACEALGQDDK PHVRQYGT.. \r
-AJKXQ PIPG.DWNGA GAHTNFSTKQ TMEGWDAIVT CCEALG..TR VHVTHYGK.. \r
-AJZJQ2 PLGDTDWNGS GMHANFSTEY MRTVGGKEYF EALMAAFDKN LHIAVYGP.. \r
-\r
-\r
-AJPMQA ..GNERRLTG KHETADINVF SWGVANRGSS IRVGRDTEKG KGYFEDRRPA \r
-AJFBQA ..GNERRLTG RHETADINTF SWGVANRGSS VRVGRDTEKG KGYFEDRRPA \r
-AJAAQ ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPS \r
-AJFBQB ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPA \r
-AJPMQ1 ..GNERRLTG KHETADINTF SWGVANRGAS VRVGRDTEKG KGYFEDRRPA \r
-AJFBQ ..GNERRLTG KHETADMNTF IWGVANRGAS IRVGRDTEKG KGYFEDRRPA \r
-AJYLNB ..GNERRLTG RHETADISTF SWGVANRGAS I......... .......... \r
-AJRZQG ..GNERRLTG RHETADINTF SWGVANRGAS VRVGRETEQG KGYFEDRRPA \r
-AJLCQB ..GNERRLTG RHETADINTF LWGVANRGAS IRVGRDTEKG KGYFEDRRPA \r
-AJRZQB ..GNERRLTG RHETADINTF KWGVANRGAS IRVGRDTEKG KGYFEDRRPA \r
-AJFBQD ..GNERRLTG KHETASINTF SWGVANRGCS IRVGRDTEKG KGYLEDRRPA \r
-AJPMQ2 ..GNERRLTG KHETASINDF SWGVANRGCS IRVGRDTEKG KGYLEDRRPA \r
-AJRZQD ..GNERRLTG LHETASIDNF SWGVANRGCS IRVGRDTEAG KGYLEDRRPA \r
-AJBHQ ..GNERRLTG LHETASISDF SWGVANRGCS IRVGRDTEAG KGYLEDRRPA \r
-AJDHQ ..GNERRLTG KHETSSMNDF SWGVANRGCS IRVGRMVPVK CGYYEDRRPS \r
-AJMSQ GLDNARALTG FHETSNINDF SAGVANRGAS IRIPRTVGQK KGYFEDRRLR \r
-AJMSQ3 .......... .......... .......... .......... .......... \r
-AJHYQ GLDNARGLTG FHETSNINDF SAGVANRSAS IRIPRTVGQK KGYFEDRRPS \r
-AJRTQ GLDNARRLTG FHETSNINDF SAGVANRSAS IRIPRIVGQK KGYFEDRRPS \r
-AJHUQ GLDNARRLTG FHETSNINDF SAGVANRSAR LRIPRTVGQK KGYFEDRRPS \r
-AJCHQ GLDNARRLTG FHETSSIHEF SAGVANRGAS IRIPRNVGHK KGYFEDRGPS \r
-AJFF2C GQDNARRLTG KHETSSINDF SAGVANRGCS IRIPRGVNDG KGYFEDRCPS \r
-AJFF1M GKDNERRLVG RLETSSIDKF SWGVANRAVS VRVPRGVATG KGYLEDRRPS \r
-AJSM2V ..GIDDRLTG LHETAPWNEY SYGVSDRGAS VRIPWQVEKG KGYIEDRRPN \r
-AJSM2H ..GIEDRLTG AHETAPWDAY SYGASDRGAS VRIPWQVEVK KGYIEDRRPN \r
-AJKXQ ..GIEDRLTG KHETAPWNKY SWGASDRGAS VRIPWAVEKK KGWLEDRRPN \r
-AJZJQ2 ..DNDKRLTG KHETAPWNKF SYGVADRGAS IRVPHSFVNY KGYLEDRRPN \r
-\r
-\r
-AJPMQA SNMDPYVVTS MIAETTILWK KP........ .........\r
-AJFBQA SNMDPYVVTS MIAETTILWK P......... .........\r
-AJAAQ SNMDPYVVTS MIADTTILWK P......... .........\r
-AJFBQB SNMDPYVVTS MIADTTILWK P......... .........\r
-AJPMQ1 SNMDPYVVTS MIAETTILLK P......... .........\r
-AJFBQ SNMDPYVVTS MIAETTLLWK P......... .........\r
-AJYLNB .......... .......... .......... .........\r
-AJRZQG SNMDPYIVTS MIAETTIIWK P......... .........\r
-AJLCQB SNMDPYVVTS MIAETTILWD NKS....... .........\r
-AJRZQB SNMDPYVVTG MIAETTLLWK QN........ .........\r
-AJFBQD SNMDPYVVTS LLAESTLLWE PTLEAEALAA QKLALKV..\r
-AJPMQ2 SNMDPYVVTA LLAESTLLWE PTLEAEALAA QKIALKV..\r
-AJRZQD SNMDPYVVTA LLAETTILWE PTLEAEVLAA KKLALKV..\r
-AJBHQ SNMDPYTVTA LLAETTILWE PTLEAEALAA KKLALKV..\r
-AJDHQ SNLDPYVVTR LLVETTLL.. .......... .........\r
-AJMSQ ANCDPYAVTE AIVRTCLLNE TGDEPFQYKN .........\r
-AJMSQ3 .......... .......... .......... .........\r
-AJHYQ ANCDPFAVTE AIVRTCLLNE TGDEPFQYKN .........\r
-AJRTQ ANCDPYAVTE AIVRTCLLNE TGDEPFQYKN .........\r
-AJHUQ ANCEPFSVTE ALIRTCLLNE TGDEPFQYKN .........\r
-AJCHQ ANCDPYAVTE ALVRTCLLNE TGDEPFEYKN .........\r
-AJFF2C SNCDPYSVVE AILRTICLDE .......... .........\r
-AJFF1M SNCDPYAVCN AIVRTCLLNE .......... .........\r
-AJSM2V ANVDPYVVTR LLVDTCCSAL EK.......A GQV......\r
-AJSM2H ANVDPYVVTR LMVDTCCTEL AR.......R EQI......\r
-AJKXQ ANMDPYLVTA LMIDTCCSAL AGDKPTLFVP SQTTPAPAS\r
-AJZJQ2 SQGDPYQIVR RS........ .......... .........\r
-\r
-\r
+++ /dev/null
-((AJRZQB:6.0347505,(AJRZQG:5.005189,(AJFBQ:5.0496607,(AJYLNB:4.8739843,((((((AJZJQ2:17.922678,(AJKXQ:13.302137,(AJSM2H:9.190935,AJSM2V:8.348928):4.237726):4.1729946):2.1668549,((AJFF1M:17.32338,AJFF2C:14.795074):1.1247139,(AJMSQ3:0.0,(AJCHQ:4.7881308,(AJHUQ:3.5035172,(AJRTQ:1.5708065,(AJHYQ:1.594532,AJMSQ:1.8223228):0.25151634):1.0522919):2.2449017):4.756546):6.748291):0.93679047):2.2975445,AJDHQ:3.1142578):7.6872816,(AJBHQ:6.8556995,AJRZQD:5.6727734):4.075513):0.63313675,(AJPMQ2:4.3359585,AJFBQD:3.6367054):5.6366634):2.04666,((AJPMQ1:4.699384,(AJFBQB:3.4119358,AJAAQ:2.5106182):0.31200266):0.88102937,(AJFBQA:2.4191017,AJPMQA:3.2756615):2.5073526):0.42850304):0.0):0.0):0.26338387):0.46177864):6.5498247,AJLCQB:6.5498247);\r
+++ /dev/null
-PileUp\r
-\r
-\r
-\r
- MSF: 487 Type: P Check: 4627 .. \r
-\r
- Name: LIP1_CANFA oo Len: 487 Check: 678 Weight: 1.00\r
- Name: LIP2_MOUSE oo Len: 487 Check: 2632 Weight: 1.00\r
- Name: LIPH_HUMAN oo Len: 487 Check: 2807 Weight: 1.00\r
- Name: LIPH_MOUSE oo Len: 487 Check: 1096 Weight: 1.00\r
- Name: LIPH_RAT oo Len: 487 Check: 1917 Weight: 1.00\r
- Name: LIPL_BOVIN oo Len: 487 Check: 3520 Weight: 1.00\r
- Name: LIPL_CAVPO oo Len: 487 Check: 9282 Weight: 1.00\r
- Name: LIPL_CHICK oo Len: 487 Check: 7040 Weight: 1.00\r
- Name: LIPL_HUMAN oo Len: 487 Check: 3879 Weight: 1.00\r
- Name: LIPL_MOUSE oo Len: 487 Check: 5123 Weight: 1.00\r
- Name: LIPL_RAT oo Len: 487 Check: 3636 Weight: 1.00\r
- Name: LIPP_HORSE oo Len: 487 Check: 3071 Weight: 1.00\r
- Name: LIPP_HUMAN oo Len: 487 Check: 243 Weight: 1.00\r
- Name: LIPP_PIG oo Len: 487 Check: 3267 Weight: 1.00\r
- Name: LIPP_RABIT oo Len: 487 Check: 5962 Weight: 1.00\r
- Name: LIPP_RAT oo Len: 487 Check: 474 Weight: 1.00\r
-\r
-//\r
-\r
-\r
-\r
-LIP1_CANFA KEVCYEQIGC FSDAEPWAG. TAIRPLKVLP WSPERIGTRF LLYTNKNP.N \r
-LIP2_MOUSE KEVCYGHLGC FSNDKPWAG. MIQRPSKIFP WSPEDIDTRF LLYTNENP.N \r
-LIPH_HUMAN SSALGQSLKP EPFGRRAQA. ......VETN KTLHEMKTRF LLFGETN... \r
-LIPH_MOUSE SSACGQGVGT EPFGRSLGA. ......TEAS KPLKKPETRF LLFQDEND.R \r
-LIPH_RAT SSACGQGVGT EPFGRNLGA. ......TEER KPLQKPEIRF LLFKDESD.R \r
-LIPL_BOVIN LDPAGPNFEY AEDRITGG.. .......... KDFRDIESKF ALRTPEDTAE \r
-LIPL_CAVPO MNIDRKILNK ALAKEKVAN. ........CQ KDYTDIESKF ARRTPENTVE \r
-LIPL_CHICK KTALLAVLCL CLRGAAGSD. ......PEAE MNFEGIESKF SLRTPAEPDE \r
-LIPL_HUMAN LAVWLQSLTA SRGGVAAAD. ........QR RDFIDIESKF ALRTPEDTAE \r
-LIPL_MOUSE LGVWLQSLTA FRGGVAAAD. ........AG RDFSDIESKF ALRTPEDTAE \r
-LIPL_RAT LGVWLQSLTA FRGGVAAAD. ........GG RDFSDIESKF ALRTPEDTAE \r
-LIPP_HORSE NEVCYERLGC FSDDSPWAG. IVERPLKILP WSPEKVNTRF LLYTNENP.D \r
-LIPP_HUMAN KEVCYERLGC FSDDSPWSG. ITERPLHILP WSPKDVNTRF LLYTNENP.N \r
-LIPP_PIG SEVCFPRLGC FSDDAPWAG. IVQRPLKILP PD.KDVDTRF LLYTNQNQ.N \r
-LIPP_RABIT LEVCYERLGC FGNRIPWSGG TLERPFSTLP STPKIVNTRF LLYTNENP.N \r
-LIPP_RAT KEVCFDKLGC FSDDAPWSG. TIDRPLKALP WSPAQINTRF LLYTNENQ.D \r
-\r
-\r
-LIP1_CANFA NFQTLLPSDP STIEASNFQT DKKTRFIIHG FIDKGE.ENW LLDMCKNMFK \r
-LIP2_MOUSE NYQIISATDP ATINASNFQL DRKTRFIIHG FIDKGE.EGW LLDMCKKMFQ \r
-LIPH_HUMAN QGCQIRINHP DTLQECGFNS SLPLVMIIHG WSVDGVLENW IWQMVAALKS \r
-LIPH_MOUSE LGCRLRPQHP ETLQECGFNS SQPLIMIIHG WSVDGLLENW IWKIVSALKS \r
-LIPH_RAT LGCQLRPQHP ETLQECGFNS SHPLVMIIHG WSVDGLLETW IWKIVGALKS \r
-LIPL_BOVIN DTCHLIPGVT ESVANCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK \r
-LIPL_CAVPO DTCHLIPGVT ESVANCHFNH SSKTFMVIHG WTVTGMYESW VPKLVAALYK \r
-LIPL_CHICK DVCYLVPGQM DSLAQCNFNH TSKTFVVIHG WTVTGMYESW VPKLVDALYK \r
-LIPL_HUMAN DTCHLIPGVA ESVATCHFNH SSKTFMVIHG WTVTGMYESW VPKLVAALYK \r
-LIPL_MOUSE DTCHLIPGLA DSVSNCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK \r
-LIPL_RAT DTCHLIPGLA DSVSNCHFNH SSKTFVVIHG WTVTGMYESW VPKLVAALYK \r
-LIPP_HORSE NFQEIV.ADP STIQSSNFNT GRKTRFIIHG FIDKGE.ESW LSTMCQNMFK \r
-LIPP_HUMAN NFQEVA.ADS SSISGSNFKT NRKTRFIIHG FIDKGE.ENW LANVCKNLFK \r
-LIPP_PIG NYQELV.ADP STITNSNFRM DRKTRFIIHG FIDKGE.EDW LSNICKNLFK \r
-LIPP_RABIT NFQEIS.ADA STIRGSNFRT DRKTRFIIHG FTDKGE.ENW LSNLCENLFQ \r
-LIPP_RAT NYQKIT.SDA SSIRNSNFKT NRKTRIIIHG FIDKGE.ENW LSDMCKNMFK \r
-\r
-\r
-LIP1_CANFA V...EEVNCI CVDWKKGSQT SYTQAANNVR VVGAQVAQML SMLSANYSYS \r
-LIP2_MOUSE V...EKVNCI CVDWKRGSRT EYTQASYNTR VLGAEIAFLV QVLSTEMGYS \r
-LIPH_HUMAN QPAQP.VNVG LVDWITLAHD HYTIAVRNTR LVGKEVAALL RWLEESVQLS \r
-LIPH_MOUSE RQSQP.VNVG LVDWISLAYQ HYTIAVQNTR IVGQDVAALL LWLEESAKFS \r
-LIPH_RAT RQSQP.VNVG LVDWISLAYQ HYAIAVRNTR VVGQEVAALL LWLEESMKFS \r
-LIPL_BOVIN R..EPDSNVI VVDWLSRAQQ HYPVSAGYTK LVGQDVAKFM NWMADEFNYP \r
-LIPL_CAVPO R..EPDSNVI VVDWLRRAQH HYPESADYTK LVGEDVARFI NWMEDEFKYS \r
-LIPL_CHICK R..EPDSNVI VVDWLVRAQQ HYPVSAAYTK LVGKDVAMFI DWMEEKFNYP \r
-LIPL_HUMAN R..EPDSNVI VVDWLSRAQE HYPVSAGYTK LVGQDVARFI NWMEEEFNYP \r
-LIPL_MOUSE R..EPDSNVI VVDWLYRAQQ HYPVSAGYTK LVGNDVARFI NWMEEEFNYP \r
-LIPL_RAT R..EPDSNVI VVDWLYRAQQ HYPVSAGYTK LVGNDVARFI NWLEEEFNYP \r
-LIPP_HORSE V...ESVNCI CVDWKSGSRT AYSQASQNVR IVGAEVAYLV GVLQSSFDYS \r
-LIPP_HUMAN V...ESVNCI CVDWKGGSRT GYTQASQNIR IVGAEVAYFV EFLQSAFGYS \r
-LIPP_PIG V...ESVNCI CVDWKGGSRT GYTQASQNIR IVGAEVAYFV EVLKSSLGYS \r
-LIPP_RABIT V...ETVNCI CVDWKGGSRT TYPQATQNIR IVGAEVAYLV GTLQSSLGYS \r
-LIPP_RAT V...ESVNCI CVDWKGGSRA TYTQATQNVR VVGAEVALLV NVLKSDLGHP \r
-\r
-\r
-LIP1_CANFA PSQVQLIGHS LGAHVAGEAG SRTPG...LG RITGLDPVEA SFQGTPEEVR \r
-LIP2_MOUSE PENVHLIPHS LGSHVAGEAG RRLEGH..VG RITGLDPAEP CFQGLPEEVR \r
-LIPH_HUMAN RSHVHLIGYS LGAHVSGFAG SSIGGTHKIG RITGLDAAGP LFEGSAPSNR \r
-LIPH_MOUSE RSKVHLIGYS LGAHVSGFAG SSMDGKNKIG RITGLDPAGP MFEGTSPNER \r
-LIPH_RAT RSKVHLIGYS LGAHVSGFAG SSMGGKRKIG RITGLDPAGP MFEGTSPNER \r
-LIPL_BOVIN LGNVHLLGYS LGAHAAGIAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR \r
-LIPL_CAVPO VDNVHLLGYS LGAHAAGVAG SRTN..TKVS RITGLDPAGP NFEYAEATSR \r
-LIPL_CHICK LNNVHLLGYS LGAHAAGIAG SLTK..KKVN RITGLDPAGP TFEYADAPIR \r
-LIPL_HUMAN LDNVHLLGYS LGAHAAGIAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR \r
-LIPL_MOUSE LDNVHLLGYS LGAHAAGVAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR \r
-LIPL_RAT LDNVHLLGYS LGAHAAGVAG SLTN..KKVN RITGLDPAGP NFEYAEAPSR \r
-LIPP_HORSE PSNVHIIGHS LGSHAAGEAG RRTNGA..VG RITGLDPAEP CFQGTPELVR \r
-LIPP_HUMAN PSNVHVIGHS LGAHAAGEAG RRTNGT..IG RITGLDPAEP CFQGTPELVR \r
-LIPP_PIG PSNVHVIGHS LGSHAAGEAG RRTNGT..IE RITGLDPAEP CFQGTPELVR \r
-LIPP_RABIT PSNIHVIGHS LGAHAAGEVG RRTNGT..IG RITGLDPAEP YFQGTPEIVR \r
-LIPP_RAT PDNVHLIGHS LGSHVAGEAG KRTFGA..IG RITGLDAAEP YFQGTPEEVR \r
-\r
-\r
-LIP1_CANFA LDPTDADFVD VIHTDAAPLI PFLGFGTSQQ MGHLDFFPNG GEEMPGCKKN \r
-LIP2_MOUSE LDPSDAMFVD VIHTDSAPII PYLGFGMSQK VGHLDFFPNG GKEIPGCQKN \r
-LIPH_HUMAN LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IGHYDFYPNG GSFQPGCHFL \r
-LIPH_MOUSE LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IAHYDFYPNG GSFQPGCHFL \r
-LIPH_RAT LSPDDANFVD AIHTFTR.EH MGLSVGIKQP IAHYDFYPNG GSFQPGCHFL \r
-LIPL_BOVIN LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG \r
-LIPL_CAVPO LSPDDAQFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GSFQPGCNIQ \r
-LIPL_CHICK LSPDDADFVD VLHTYTR.GS PDRSIGIQKP VGHIDIYPNG GGFQPGCNLG \r
-LIPL_HUMAN LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG \r
-LIPL_MOUSE LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG \r
-LIPL_RAT LSPDDADFVD VLHTFTR.GS PGRSIGIQKP VGHVDIYPNG GTFQPGCNIG \r
-LIPP_HORSE LDPSDAQFVD VIHTDIAPFI PNLGFGMSQT AGHLDFFPNG GKEMPGCQKN \r
-LIPP_HUMAN LDPSDAKFVD VIHTDGAPIV PNLGFGMSQV VGHLDFFPNG GVEMPGCKKN \r
-LIPP_PIG LDPSDAKFVD VIHTDAAPII PNLGFGMSQT VGHLDFFPNG GKQMPGCQKN \r
-LIPP_RABIT LDPSDAQFVD VIHTDAAPMV PNLGFGMSQT VGHLDFFPNG GKEMPGCQKN \r
-LIPP_RAT LDPTDAQFVD AIHTDAAPII PNLGFGMSQT VGHLDFFPNG GMEMPGCQKN \r
-\r
-\r
-LIP1_CANFA ALSQIVDLDG IWEGTRDFVA CNHLRSYKYY SESILNPDG. FASYPCASYR \r
-LIP2_MOUSE ILSTIVDING IWEGTRNFAA CNHLRSYKYY ASSILNPDG. FLGYPCSSYE \r
-LIPH_HUMAN ELYRHIAQHG FNAITQ.TIK CSHERSVHLF IDSLLHAGTQ SMAYPCGDMN \r
-LIPH_MOUSE ELYKHIAEHG LNAITQ.TIK CAHERSVHPF IDSLQHSDLQ SIGFQCSDMG \r
-LIPH_RAT ELYKHIAEHG LNAITQ.TIN CAHERSVHLF IDSLQHSNLQ NTGFQCSNMD \r
-LIPL_BOVIN EALRVIAERG LGDVDQ.LVK CSHERSVHLF IDSLLNEENP SKAYRCNSKE \r
-LIPL_CAVPO DALRVISQKG FGDMDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE \r
-LIPL_CHICK EALRLIAEKG FSDVDQ.LVK CSHERSIHLF IDSLLYEEKP SMAYRCNTKE \r
-LIPL_HUMAN EAIRVIAERG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCSSKE \r
-LIPL_MOUSE EAIRVIAERG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE \r
-LIPL_RAT EAIRVIAEKG LGDVDQ.LVK CSHERSIHLF IDSLLNEENP SKAYRCNSKE \r
-LIPP_HORSE VLSQIVDIDG IWQGTRDFAA CNHLRSYKYY TDSILNPDG. FAGFSCASYS \r
-LIPP_HUMAN ILSQIVDIDG IWEGTRDFAA CNHLRSYKYY TDSIVNPDG. FAGFPCASYN \r
-LIPP_PIG ILSQIVDIDG IWEGTRDFVA CNHLRSYKYY ADSILNPDG. FAGFPCDSYN \r
-LIPP_RABIT VLSQIVDING VWEGTRDFVA CNHLRSYKYY ADSIVNPNG. FAGFSCASYT \r
-LIPP_RAT ILSQIVDIDG IWEGTRDFAA CNHLRSYKYY TDSIVNPTG. FSGFSCSSYN \r
-\r
-\r
-LIP1_CANFA AFESNKCFPC PDQGCPQMGH YADKFAVKTS DETQKYFLNT GDSSNFARWR \r
-LIP2_MOUSE KFQHNDCFPS PEQGCPKMGH YADQFEGKTA TVEQTFFLNT ADTGNFTRWR \r
-LIPH_HUMAN SFSQGLCLSC KKGRCNTLGY HVRQEPRSKS ...KRLFLVT RAQSPFKVYH \r
-LIPH_MOUSE SFSQGLCLSC KKGRCNTLGY DIRKDRSGKS ...KRLFLIT RAQSPFKVYH \r
-LIPH_RAT SFSQGLCLNC KKGRCNSLGY DIRRIGHVKS ...KTLFLIT RAQSPFKVYH \r
-LIPL_BOVIN AFEKGLCLSC RKNRCNNMGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPL_CAVPO AFEKGLCLSC RKNRCNNVGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPL_CHICK AFEKGLCLSC RKNRCNNLGY KVNRVRTKRN ...TKMYLKT RAQMPYKVFH \r
-LIPL_HUMAN AFEKGLCLSC RKNRCNNLGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPL_MOUSE AFEKGLCLSC RKNRCNNLGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPL_RAT AFEKGLCLSC RKNRCNNVGY EINKVRAKRS ...SKMYLKT RSQMPYKVFH \r
-LIPP_HORSE DFTANKCFPC SSEGCPQMGH YADRFPGRTK GVGQLFYLNT GDASNFARWR \r
-LIPP_HUMAN VFTANKCFPC PSGGCPQMGH YADRYPGKTN DVGQKFYLDT GDASNFARWR \r
-LIPP_PIG VFTANKCFPC PSEGCPQMGH YADRFPGKTN GVSQVFYLNT GDASNFARWR \r
-LIPP_RABIT AFSANKCFPC SN.GCPQMGH YADRFSRKTD GVGQTFYLNT GDSSNFARWR \r
-LIPP_RAT VFSANKCFPC GSEGCPQMGH YADKYPGKTK ELYQKFYLNT GDKSNFARWR \r
-\r
-\r
-LIP1_CANFA YGVSITLSG. ..KR.ATGQA KVALFGSKGN THQFNIFKGI .LKPGSTHSN \r
-LIP2_MOUSE YKVSVTLSGP ..KK.LSGYI LVALYGCNAN SKQYEVFKGS .LQPEARYIR \r
-LIPH_HUMAN YQLKIQFINQ TETP.IQTTF TMSLLGTKEK MQKIPITLGK GIASNKTYSF \r
-LIPH_MOUSE YQFKIQFINQ IEKP.VEPTF TMSLLGTKEE IKRIPITLGE GITSNKTYSF \r
-LIPH_RAT YQFKIQFINQ MEKP.MEPTF TMTLLGTKEE IKKIPITLGE GITSNKTYSL \r
-LIPL_BOVIN YQVKIHFSGT ESNTYTNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF \r
-LIPL_CAVPO YQVKIYFSGT ETTTYTNQAF EISLYGTVAE SENIPFTLPE .VSANNTYSF \r
-LIPL_CHICK YQVKIHFFGK TNVTKVDQPF LISLYGTLDE SENIPFTLPE .VSSNKTFSF \r
-LIPL_HUMAN YQVKIHFSGT ESETHTNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF \r
-LIPL_MOUSE YQVKIHFSGT ENGKQHNQAF EISLYGTVAE SENIPFTLPE .VSTNKTYSF \r
-LIPL_RAT YQVKIHFSGT ENDKQNNQAF EISLYGTVAE SENIPFTLPE .VATNKTYSF \r
-LIPP_HORSE YRVDVTLSG. ..KK.VTGHV LVSLFGNKGN SRQYEIFQGT .LKPDNTYSN \r
-LIPP_HUMAN YKVSVTLSG. ..KK.VTGHI LVSLFGNKGN SKQYEIFKGT .LKPDSTHSN \r
-LIPP_PIG YKVSVTLSG. ..KK.VTGHI LVSLFGNEGN SRQYEIYKGT .LQPDNTHSD \r
-LIPP_RABIT YQVAVTLSG. ..RR.VTGHV LVSLYGSKGN SKQYEIFTGL .LKPGDTHLN \r
-LIPP_RAT YQVTVTLSG. ..QK.VTGHI LVSLFGNGGN SKQYEVFKGS .LHPGDTHVK \r
-\r
-\r
-LIP1_CANFA EFDAKLDVGT IEKVKFLWNN N..VVNPTFP KVG....... ........AA \r
-LIP2_MOUSE DIDVDVNVGE IQKVKFLWNN K..VINLFRP TMG....... ........AS \r
-LIPH_HUMAN LITLDVDIGE LIMIKFKWEN S..AVWANVW DTVQTIIPWS TGPRHSGLVL \r
-LIPH_MOUSE LITLDKDIGE LILLKFKWEN S..AVWANVW NTVQTIMLWG IEPHHSGLIL \r
-LIPH_RAT LITLNKDIGE LIMLKFKWEN S..AVWANVW NTVQTIMLWD TEPHYAGLIV \r
-LIPL_BOVIN LLYTEVDIGE LLMLKLKWIS DSYFSWSNWW SSP....... ......GFDI \r
-LIPL_CAVPO LIYTEVDIGE LLMLKLKWIT ESYFSWSSWW GRP....... ......TFTI \r
-LIPL_CHICK LIYTEVDIGD LLMLKLQWEK DTFFSWSDWW TPF....... ......AFTI \r
-LIPL_HUMAN LIYTEVDIGE LLMLKLKWKS DSYFSWSDWW SSP....... ......GFAI \r
-LIPL_MOUSE LIYTEVDIGE LLMMKLKWMS DSYFSWPDWW SSP....... ......SFVI \r
-LIPL_RAT LIYTEVDIGE LLMMKLKWKN DSYFRWSDWW SSP....... ......SFVI \r
-LIPP_HORSE EFDSDVEVGD LEKVKFIWYN N..VINLTLP KVG....... ........AS \r
-LIPP_HUMAN EFDSDVDVGD LQMVKFIWYN N..VINPTLP RVG....... ........AS \r
-LIPP_PIG EFDSDVEVGD LQKVKFIWYN NN.VINPTLP RVG....... ........AS \r
-LIPP_RABIT EFDSDVDVGD VQKVKFVWYN N..VINPTLP KVG....... ........AS \r
-LIPP_RAT EFDSDMDVGD LQKVKFIWYN N..VINPTLP KVG....... ........AS \r
-\r
-\r
-LIP1_CANFA KITVQK.GEE KTVHSFCSES TVR....EDV LLTLTPC\r
-LIP2_MOUSE QITLQR.AKD GKEFNFCTSN TVH....EDV LQSLYPC\r
-LIPH_HUMAN KTIRVKAGET QQRMTFCSEN TDDLLLRPTQ EKIFVKC\r
-LIPH_MOUSE KTIWVKAGET QQRMTFCPEN LDDLQLHPSQ EKVFVNC\r
-LIPH_RAT KTIWVKAGET QQRMTFCPDN VDDLQLHPTQ EKVFVKC\r
-LIPL_BOVIN GKIRVKAGET QKKVIFCSRE KMSYLQKGKS PVIFVKC\r
-LIPL_CAVPO EKIRVKAGET QKKIVFCSRE KVSKLQKGKE APVFVKC\r
-LIPL_CHICK QRVRVKSGET QKKVVFCSRD GSSRLGKGEE AAIFVKC\r
-LIPL_HUMAN QKIRVKAGET QKKVIFCSRE KVSHLQKGKA PAVFVKC\r
-LIPL_MOUSE ERIRVKAGET QKKVIFCARE KVSHLQKGKD SAVFVKC\r
-LIPL_RAT EKIRVKAGET QKKVIFCARE KVSHLQKGKD AAVFVKC\r
-LIPP_HORSE KITVER.NDG .SVFNFCSEE TVR....EDV LLTLTAC\r
-LIPP_HUMAN KIIVET.NVG .KQFNFCSPE TVR....EEV LLTLTPC\r
-LIPP_PIG KITVER.NDG .KVYDFCSQE TVR....EEV LLTLNPC\r
-LIPP_RABIT QITVEQ.NDG .RVFKFCSTD TVR....EDI LLTLTPC\r
-LIPP_RAT RISVER.NDG .RVFNFCSQD TVR....EDV LLTLSAC\r
-\r
-\r
+++ /dev/null
-PileUp\r
-\r
-\r
-\r
- MSF: 279 Type: P Check: 9995 .. \r
-\r
- Name: KYBOA oo Len: 279 Check: 4492 Weight: 1.00\r
- Name: TRBOTR oo Len: 279 Check: 6670 Weight: 1.00\r
- Name: ELPG oo Len: 279 Check: 6037 Weight: 1.00\r
- Name: PRRTG oo Len: 279 Check: 3057 Weight: 1.00\r
- Name: KQHUP oo Len: 279 Check: 6499 Weight: 1.00\r
- Name: TRSMG oo Len: 279 Check: 3240 Weight: 1.00\r
-\r
-//\r
-\r
-\r
-\r
-KYBOA .CGVP..... AIQPVLSGLS .........R IVNGEEAVPG SWPWQVSLQD \r
-TRBOTR .......... .....VDDDD .........K IVGGYTCGAN TVPYQVSLN. \r
-ELPG .......... .......... .......... VVGGTEAQRN SWPSQISLQY \r
-PRRTG .......... .......... .......... IIGGVESIPH SRPYMAHLDI \r
-KQHUP AYGTQGSSGY SLRLCNTGDN SVCTTKTSTR IVGGTNSSWG EWPWQVSLQV \r
-TRSMG .......... .......... .......... VVGGTRAAQG EFPFMVRLS. \r
-\r
-\r
-KYBOA K...TGFHFC GGSLINENWV VTAAHCG... ..VTTSDVVV AGEFDQGSSS \r
-TRBOTR ....SGYHFC GGSLINSQWV VSAAHCY... ..KSGIQVRL G.EDNINVVE \r
-ELPG RSGSSWAHTC GGTLIRQNWV MTAAHCVD.. .RELTFRVVV G.EHNLNQNN \r
-PRRTG VTEKGLRVIC GGFLISRQFV LTAAHCK... ..GREITVIL G.AHDVRKRE \r
-KQHUP K.LTAQRHLC GGSLIGHQWV LTAAHCFDGL PLQDVWRIYS G.ILNLSDIT \r
-TRSMG .......MGC GGALYAQDIV LTAAHCVS.. ..GSGNNTSI TATGGVVDLQ \r
-\r
-\r
-KYBOA EKIQKLKIAK VFKNSKYNSL TINN..DITL LKLSTAASFS QTVSAVCLPS \r
-TRBOTR GNEQFISASK SIVHPSYNSN TLNN..DIML IKLKSAASLN SRVASISLPT \r
-ELPG GTEQYVGVQK IVVHPYWNTD DVAAGYDIAL LRLAQSVTLN SYVQLGVLPR \r
-PRRTG STQQKIKVEK QIIHESYNSV PNLH..DIML LKLEKKVELT PAVNVVPLPS \r
-KQHUP KDTPFSQIKE IIIHQNYKVS EGNH..DIAL IKLQAPLNYT EFQKPICLPS \r
-TRSMG S.AVKVRSTK VLQAPGYNGT G.K...DWAL IKLAQPINQ. P.....TLKI \r
-\r
-\r
-KYBOA ASDDFAAGTT CVTTGWGLTR YTNANTPDRL QQASLPLLSN TNCKK..YWG \r
-TRBOTR S..CASAGTQ CLISGWGNTK SSGTSYPDVL KCLKAPILSD SSCKS..AYP \r
-ELPG AGTILANNSP CYITGWGLTR .TNGQLAQTL QQAYLPTVDY AICSSSSYWG \r
-PRRTG PSDFIHPGAM CWAAGWGKTG .VRDPTSYTL REVELRIMDE KACVD...YR \r
-KQHUP KGDTSTIYTN CWVTGWGFSK .EKGEIQNIL QKVNIPLVTN EECQKR.YQD \r
-TRSMG ATTTAYNQGT FTVAGWGANR .EGGSQQRYL LKANVPFVSD AACRS.AYGN \r
-\r
-\r
-KYBOA TKIKDAMICA G...ASGVSS .CMGDSGGPL VCKK.NGAWT LVGIVSWGS. \r
-TRBOTR GQITSNMFCA GY.LEGGKDS .CQGDSGGPV VCS...G..K LQGIVSWGS. \r
-ELPG STVKNSMVCA G...GNGVRS GCQGDSGGPL HCLV.NGQYA VHGVTSFVSR \r
-PRRTG YYEYKFQVCV G..SPTTLRA AFMGDSGGPL LCA...G..V AHGIVSYGH. \r
-KQHUP YKITQRMVCA GY.KEGGKDA .CKGDSGGPL VCKH.NGMWR LVGITSWGE. \r
-TRSMG ELVANEEICA GYPDTGGVDT .CQGDSGGPM FRKDNADEWI QVGIVSWGY. \r
-\r
-\r
-KYBOA .STCSTSTPG VYARVTALVN WVQQTLAAN\r
-TRBOTR .GCAQKNKPG VYTKVCNYVS WIKQTIASN\r
-ELPG LGCNVTRKPT VFTRVSAYIS WINNVIASN\r
-PRRTG ...PDAKPPA IFTRVSTYVP TINAVIN..\r
-KQHUP .GCARREQPG V......... .........\r
-TRSMG .GCARPGYPG VYTEVSTFAS AIASAARTL\r
-\r
-\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
-<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
-<head>\r
-<!-- InstanceBeginEditable name="doctitle" -->\r
-<TITLE>JalView - Java alignment editor</TITLE>\r
-<!-- InstanceEndEditable -->\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
-<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->\r
-<style type="text/css">\r
-<!--\r
-td {\r
- font-family: Geneva, Arial, Helvetica, sans-serif;\r
- font-size: 12px;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<div align="left">\r
- <table border="0">\r
- <tr>\r
- <td width="700" ><center>\r
- <table width="550" border="0">\r
- <tr>\r
- <td width="45%"><div align="center"><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/index.html"><img src="../snap22med.gif" width="291" height="116" border="0" align="absmiddle"></a></div></td>\r
- <td width="55%"><div align="center"><font size="+6"><strong><font face="Geneva, Arial, Helvetica, sans-serif">Jalview\r
- </font></strong></font> </div>\r
- <div align="center"><font size="3" face="Geneva, Arial, Helvetica, sans-serif">a\r
- multiple alignment editor</font> </div></td>\r
- </tr>\r
- </table>\r
- </center></td>\r
- </tr>\r
- </table>\r
- <br>\r
- <table border="0">\r
- <tr>\r
- <td width="197" valign="top" nowrap> <p><strong>Downloads</strong></p>\r
- <ul>\r
- <li><a href="index.html">Jalview</a></li>\r
- </ul>\r
- <strong>Examples</strong> <ul>\r
- <li><a href="examples/applets.html">Applet</a></li>\r
- <li><a href="examples/examples.html">Application</a></li>\r
- </ul>\r
- <strong>Reference</strong> <ul>\r
- <li> <a href="../jalview.pdf" target="_blank">"The Jalview Java<br>\r
- Alignment Editor,"<br>\r
- </a></li>\r
- <a href="../jalview.pdf"><em>Bioinformatics</em>, 12, 426-7</a>\r
- </ul>\r
- <strong>Source Code</strong> <ul>\r
- <li>Jalview 2</li>\r
- </ul>\r
- <p><strong>Feedback</strong></p>\r
- <p> <img src="../help.gif" width="151" height="43"> </p>\r
- <p><br>\r
- <a href="http://www.bbsrc.ac.uk/"> <img border="0"src="../bbsrc.jpg"></a>\r
- </p></td>\r
- <td width="499" valign="top"><!-- InstanceBeginEditable name="Contents" -->\r
- <p>Key features of Jalview Version 2:\r
- <ul>\r
- <li>Remote tools implemented as web services</li>\r
- <li>Remote alignments (<a href="http://www.ebi.ac.uk/clustalw/" target="CLUSTAL">Clustal</a>, <a href="http://www.drive5.com/muscle/" target="MUSCLE">Muscle</a>...)</li>\r
- <li>Remote alignment annotation (<a href="http://www.compbio.dundee.ac.uk/~www-jpred/" target="JPRED">JPred Secondary Structure Prediction</a>)</li>\r
- <li>Printing</li>\r
- <li>PNG, HTML, Encapsulated PostScript output</li>\r
- </ul>\r
- <p>Current development allows the Jalview Application to be distributed\r
- using Java Web Start which is installed with <a href="http://www.java.com/en/download/" target="JAVA">Java.</a>\r
- Each time the application is started via Java Web Start an automatic\r
- update is performed so that you will always be running the latest code.<br>\r
- <br>\r
- N.B. if you have a local installation of Java and clicking on the link\r
- below prompts the question "Open using application...", locate\r
- your installation of Java Web Start - its called "javaws". Your web browser will now associate .jnlp\r
- files with Java Web Start<br>\r
- <br>\r
- Try it now.\r
- <center>\r
- <h2><a href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/version2/webstart/JalviewX.jnlp">Start\r
- Jalview</a> </h2>\r
- <p> </p>\r
- </center>\r
- If you are having difficulties installing Java or would prefer not to\r
- use Java Web Start you could try installing Jalview from the following\r
- link.\r
- <p>\r
- <center>\r
- <h2><a target="NEW" href="Web_Installers/install.htm">Install with InstallAnywhere</a>\r
- </h2>\r
- </center>\r
- <!-- InstanceEndEditable -->\r
- </td>\r
- </tr>\r
- </table>\r
-</div>\r
-</body>\r
-<!-- InstanceEnd --></html>\r
+++ /dev/null
-<?xml version="1.0" encoding="utf-8"?> \r
-<jnlp codebase="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/version2/webstart" \r
- href="http://www.compbio.dundee.ac.uk/~andrew/JalviewWebsite/version2/webstart/JalviewX.jnlp">\r
- <information>\r
- <title>Jalview</title>\r
- <vendor>The Barton Group</vendor>\r
- <homepage href="www.jalview.org"/>\r
- <description>Jalview Multiple Alignment Editor</description>\r
- <description kind="short">Jalview</description>\r
- <icon href="logo_big.gif"/>\r
- <association mime-type="application-x/ext-file" extensions="fa"/>\r
- <association mime-type="application-x/ext-file" extensions="fasta"/>\r
- <association mime-type="application-x/ext-file" extensions="fastq"/>\r
- <association mime-type="application-x/ext-file" extensions="blc"/>\r
- <association mime-type="application-x/ext-file" extensions="msf"/>\r
- <association mime-type="application-x/ext-file" extensions="pfam"/>\r
- <association mime-type="application-x/ext-file" extensions="aln"/>\r
- <association mime-type="application-x/ext-file" extensions="pir"/>\r
- </information>\r
- <resources>\r
- <j2se version="1.3+"/>\r
- <jar href="JalviewX.jar"/>\r
- <jar href="regex.jar"/>\r
- <jar href="jhall.jar"/>\r
- <jar href="axis.jar"/>\r
- <jar href="jaxrpc.jar"/>\r
- <jar href="commons-logging.jar"/>\r
- <jar href="commons-discovery.jar"/>\r
- <jar href="saaj.jar"/> \r
- <jar href="wsdl4j.jar"/>\r
- <jar href="log4j-1.2.8.jar"/>\r
- <jar href="mail.jar"/>\r
- <jar href="activation.jar"/>\r
- <jar href="xercesImpl.jar"/>\r
- <jar href="castor.zip"/>\r
- <jar href="xml-apis.jar"/>\r
- </resources>\r
- <application-desc main-class="jalview.bin.Jalview"/>\r
- <security>\r
- <all-permissions/>\r
- </security>\r
-</jnlp>\r
-\r
git://source.jalview.org / jalview.git / commitdiff
