3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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6 * This file is part of Jalview.
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11 * of the License, or (at your option) any later version.
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14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Alignment Fileformats</title>
24 <style type="text/css">
35 <strong>Alignment File Formats</strong>
36 <p>Jalview understands a wide range of sequence alignment formats.
37 In order to determine which format has been used for an alignment,
38 Jalview tries to detect some text or formatting unique to one of the
40 <table width="100%" border="1">
42 <td width="17%">Format</td>
43 <td width="60%">Unique File Feature</td>
44 <td width="23%">File Extension</td>
46 <td width="17%">FASTA</td>
47 <td width="60%">>SequenceName<br> THISISASEQUENCE<br></td>
48 <td width="23%">.fa, .fasta</td>
51 <td width="17%">MSF</td>
52 <td width="60%">!! AA_MULTIPLE_ALIGNMENT 1.0<br> <em>..</em><br>
54 <td width="23%">.msf</td>
57 <td width="17%">CLUSTALW</td>
58 <td width="60%">CLUSTAL</td>
59 <td width="23%">.aln</td>
62 <td width="17%">PILEUP</td>
63 <td width="60%">PileUp</td>
67 <td width="17%">PIR</td>
68 <td width="60%">>P1;</td>
69 <td width="23%">.pir</td>
72 <td width="17%">BLC</td>
73 <td width="60%">>Seq1<br> >Seq2
75 <td width="23%">.blc</td>
78 <td width="17%">PFAM</td>
79 <td width="60%">SequenceName THISISASEQUENCE</td>
80 <td width="23%">.pfam</td>
83 <td width="17%">Stockholm</td>
84 <td width="60%"># STOCKHOLM VersionNumber<br> <em>...</em><br>//
86 <td width="23%">.stk, .sto</td>
89 <td width="17%">Phylip</td>
90 <td width="60%">Line starts with two numbers separated by
91 white space<br> <em>...</em><br>//
93 <td width="23%">.phy</td>
96 <td width="17%">EMBL</td>
97 <td width="60%">Line starts with ID, followed by a space, and
98 is followed by a 7 character identifier terminated with a
100 <td width="23%">.txt</td>
103 <td width="17%">GenBank</td>
104 <td width="60%">Line starts with LOCUS
106 <td width="23%">.gb,.gbk</td>
109 <td width="17%">JSON</td>
110 <td width="60%">Data starts with '{' <br>Data ends with
112 href="../features/bioJsonFormat.html">BioJSON</a> for more
113 infomation about the Jalview JSON format <br></td>
114 <td width="23%">.json</td>
119 The file extensions are used to associate Jalview alignment icons
120 with alignment files: <img src="file.png" width=12 height=12>