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-<html>
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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
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- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Input/Output</title>
-</head>
-<body>
- <p>
- <strong>Input</strong>
- </p>
- <p>Jalview can read alignment files in any of the following
- standard formats:</p>
- <p>
- <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
- NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
- </p>
- <p>
- Additionally, whole sets of coloured and annotated alignments and
- trees can be read from a <a href="../features/jalarchive.html">Jalview
- (jar) format</a> file using <strong>Desktop→Load
- Project</strong>.
- </p>
- <p>
- Press "Control O" to open a file browser, or use the <strong>Desktop→Input
- Alignment</strong> menu to read in alignments from:
- </p>
- <ul>
- <li><strong>From File</strong>: the local file system</li>
- <li><strong>From URL</strong>: the web (please use the full
- url)</li>
- <li><strong>from Textbox</strong>: a copy and paste into the
- "Cut & Paste" text window</li>
- </ul>
- <p>
- Jalview will try to recognise the file type automatically (using
- some special <a href="fileformats.html">features</a>). If a file is
- of an unknown format or there is any other error reading the
- alignment file then you will be given an error message. If you think
- Jalview really should be able to read your file, then send an email
- containing the problem file to help@jalview.org.
- </p>
- <p>
- Jalview can also read Jalview specific files for <a
- href="../features/featuresFormat.html">sequence features</a>
- and <a href="../features/annotationsFormat.html">alignment
- annotation</a>.
- </p>
- <p>
- <strong>Output</strong>
- </p>
- <p>
- Each alignment, whether it is the original or an edited version may
- be saved in the standard formats using <strong>File→Save
- As</strong>
- </p>
- <p>
- <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
- NBRF/PIR, Pfam/Stockholm</em>
- </p>
- Jalview will by default append the sequence start and end to each
- sequence name, in the format /start-end. If you do not want this
- behaviour for a particular file output, open the "Output"
- tab on the
- <a href="../features/preferences.html">Preferences</a> window where
- you can select which file formats you want to append the start and end
- sequence positions for. In the case of PIR format, the output tab also
- contains a switch for turning on the output of Modeller style
- structured description lines.
- <p>
- Quantitative and symbolic <a href="../features/annotation.html">alignment
- annotation</a> can be exported as a comma separated value file by
- right clicking on an annotation row under the alignment.
- </p>
- <p>
- You can also save the current set of alignments and their colours,
- annotations and trees in a Jalview archive file using <strong>Desktop→Save
- project</strong>.<br>The project data includes the state of any open
- structure viewers (Jmol, and <em>since Jalview 2.9</em> also Chimera
- and Varna).
- </p>
- <p> </p>
-</body>
-</html>
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