help/html/io/fileformats.html

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   3 <title>Alignment Fileformats</title>
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  14 <p><strong>Alignment Fileformats</strong>
  15 <p>Jalview understands a wide range of sequence alignment formats. In
  16 order to determine which format has been used for an alignment,
  17 jalview tries to detect some text or formatting unique to one of the formats:
  18 </p>
  19 <table width="100%" border="1">
  20 <tr><td width="17%">Format</td>
  21 <td width="60%">Unique File Feature</td>
  22 <td width="23%">File Extension</td>
  23 <tr>
  24 <td width="17%">FASTA</td>
  25 <td width="60%">&gt;SequenceName<br>
  26 THISISASEQENCE<br></td>
  27 <td width="23%">.fa, .fasta</td>
  28 </tr><tr><td width="17%">MSF</td>
  29 <td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br>
  30 <em>..</em><br>
  31 //<br></td>
  32 <td width="23%">.msf</td>
  33 </tr><tr><td width="17%">CLUSTALW</td>
  34 <td width="60%">CLUSTAL</td>
  35 <td width="23%">.aln</td>
  36 </tr><tr><td width="17%">PILEUP</td>
  37 <td width="60%">PileUp</td>
  38 <td width="23%"></td>
  39 </tr><tr><td width="17%">PIR</td>
  40 <td width="60%">&gt;P1;</td>
  41 <td width="23%">.pir</td>
  42 </tr><tr><td width="17%">BLC</td>
  43 <td width="60%">&gt;Seq1<br>
  44 &gt;Seq2</td>
  45 <td width="23%">.blc</td>
  46 </tr><tr><td width="17%">PFAM</td>
  47 <td width="60%">SequenceName THISISASEQENCE</td>
  48 <td width="23%">.pfam</td>
  49 </tr>
  50 </table>
  51 <p>The file extensions are used to associate jalview alignment icons
  52 with alignment files: <img src="file.png" width=12 height=12 >
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