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>Input/Output</title>
27 <strong>Input</strong>
29 <p>Jalview can read alignment files in any of the following
32 <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
33 NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
36 The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
37 of these file formats.
40 Additionally, whole sets of coloured and annotated alignments and
41 trees can be read from a <a href="../features/jalarchive.html">Jalview
42 (jar) format</a> file using <strong>Desktop→Load
46 Press "Control O" to open a file browser, or use the <strong>Desktop→Input
47 Alignment</strong> menu to read in alignments from:
50 <li><strong>From File</strong>: the local file system</li>
51 <li><strong>From URL</strong>: the web (please use the full
53 <li><strong>from Textbox</strong>: a copy and paste into the
54 "Cut & Paste" text window</li>
57 Jalview will try to recognise the file type automatically (using
58 some special <a href="fileformats.html">features</a>). If a file is
59 of an unknown format or there is any other error reading the
60 alignment file then you will be given an error message. If you think
61 Jalview really should be able to read your file, then send an email
62 containing the problem file to help@jalview.org.
65 Jalview can also read Jalview specific files for <a
66 href="../features/featuresFormat.html"
67 >sequence features</a> and <a
68 href="../features/annotationsFormat.html"
69 >alignment annotation</a>.
72 <strong>Output</strong>
75 Each alignment, whether it is the original or an edited version may
76 be saved in the standard formats using <strong>File→Save
80 <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
81 NBRF/PIR, Pfam/Stockholm</em>
83 Jalview will by default append the sequence start and end to each
84 sequence name, in the format /start-end. If you do not want this
85 behaviour for a particular file output, open the "Output"
87 <a href="../features/preferences.html">Preferences</a> window where
88 you can select which file formats you want to append the start and end
89 sequence positions for. In the case of PIR format, the output tab also
90 contains a switch for turning on the output of Modeller style
91 structured description lines.
93 Quantitative and symbolic <a href="../features/annotation.html">alignment
94 annotation</a> can be exported as a comma separated value file by
95 right clicking on an annotation row under the alignment.
98 You can also save the current set of alignments and their colours,
99 annotations and trees in a Jalview archive file using <strong>Desktop→Save
100 project</strong>.<br>The project data includes the state of any open
101 structure viewers (Jmol, and <em>since Jalview 2.9</em> also Chimera