<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>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:
-</p>
-<table width="100%" border="1">
-<tr><td width="17%">Format</td>
-<td width="60%">Unique File Feature</td>
-<td width="23%">File Extension</td>
-<tr>
-<td width="17%">FASTA</td>
-<td width="60%">>SequenceName<br>
-THISISASEQENCE<br></td>
-<td width="23%">.fa, .fasta</td>
-</tr><tr><td width="17%">MSF</td>
-<td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br>
-<em>..</em><br>
-//<br></td>
-<td width="23%">.msf</td>
-</tr><tr><td width="17%">CLUSTALW</td>
-<td width="60%">CLUSTAL</td>
-<td width="23%">.aln</td>
-</tr><tr><td width="17%">PILEUP</td>
-<td width="60%">PileUp</td>
-<td width="23%"></td>
-</tr><tr><td width="17%">PIR</td>
-<td width="60%">>P1;</td>
-<td width="23%">.pir</td>
-</tr><tr><td width="17%">BLC</td>
-<td width="60%">>Seq1<br>
->Seq2</td>
-<td width="23%">.blc</td>
-</tr><tr><td width="17%">PFAM</td>
-<td width="60%">SequenceName THISISASEQENCE</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>
-</table>
-<p>The file extensions are used to associate jalview alignment icons
-with alignment files: <img src="file.png" width=12 height=12 >
-</p>
+ <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:</p>
+ <table width="100%" border="1">
+ <tr>
+ <td width="17%">Format</td>
+ <td width="60%">Unique File Feature</td>
+ <td width="23%">File Extension</td>
+ <tr>
+ <td width="17%">FASTA</td>
+ <td width="60%">>SequenceName<br> 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> <em>..</em><br>
+ //<br></td>
+ <td width="23%">.msf</td>
+ </tr>
+ <tr>
+ <td width="17%">CLUSTALW</td>
+ <td width="60%">CLUSTAL</td>
+ <td width="23%">.aln</td>
+ </tr>
+ <tr>
+ <td width="17%">PILEUP</td>
+ <td width="60%">PileUp</td>
+ <td width="23%"></td>
+ </tr>
+ <tr>
+ <td width="17%">PIR</td>
+ <td width="60%">>P1;</td>
+ <td width="23%">.pir</td>
+ </tr>
+ <tr>
+ <td width="17%">BLC</td>
+ <td width="60%">>Seq1<br> >Seq2
+ </td>
+ <td width="23%">.blc</td>
+ </tr>
+ <tr>
+ <td width="17%">PFAM</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
+ 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
+ with alignment files: <img src="file.png" width=12 height=12>
+ </p>
</body>
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