3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
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.
18 * You should have received a copy of the GNU General Public License
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%">JSON</td>
97 <td width="60%">Data starts with '{' <br>Data ends with
99 href="../features/bioJsonFormat.html">BioJSON</a> for more
100 infomation about the Jalview JSON format <br></td>
101 <td width="23%">.json</td>
106 The file extensions are used to associate Jalview alignment icons
107 with alignment files: <img src="file.png" width=12 height=12>