<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
</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>
<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 infomation about the 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>
git://source.jalview.org / jalview.git / blobdiff