<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<head>
<title>Alignment Fileformats</title>
<style type="text/css">
</head>
<body>
-<p><strong>Alignment Fileformats</strong>
+<p><strong>Alignment File Formats</strong>
<p>Jalview understands a wide range of sequence alignment formats. In
order to determine which format has been used for an alignment,
-jalview tries to detect some text or formatting unique to one of the formats:
+Jalview tries to detect some text or formatting unique to one of the formats:
</p>
<table width="100%" border="1">
<tr><td width="17%">Format</td>
<tr>
<td width="17%">FASTA</td>
<td width="60%">>SequenceName<br>
-THISISASEQENCE<br></td>
+THISISASEQUENCE<br></td>
<td width="23%">.fa, .fasta</td>
</tr><tr><td width="17%">MSF</td>
<td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br>
>Seq2</td>
<td width="23%">.blc</td>
</tr><tr><td width="17%">PFAM</td>
-<td width="60%">SequenceName THISISASEQENCE</td>
+<td width="60%">SequenceName THISISASEQUENCE</td>
<td width="23%">.pfam</td>
+</tr><tr>
+<td width="17%">Stockholm</td>
+<td width="60%"># STOCKHOLM VersionNumber<br>
+<em>...</em><br>//</td>
+<td width="23%">.stk, .sto</td>
+</tr><tr>
+<td width="17%">Phylip</td>
+<td width="60%">Line starts with two numbers separated by white space<br>
+<em>...</em><br>//</td>
+<td width="23%">.phy</td>
+</tr>
+<tr>
+<td width="17%">JSON</td>
+<td width="60%">Data starts with '{' <br>Data ends with '}' <br><br>See <a href="../features/bioJsonFormat.html">BioJson</a> for more info about Jalview JSON format <br></td>
+<td width="23%">.json</td>
</tr>
</table>
-<p>The file extensions are used to associate jalview alignment icons
+<p>The file extensions are used to associate Jalview alignment icons
with alignment files: <img src="file.png" width=12 height=12 >
</p>
</body>