+ * 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>
+ The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
+ of these file formats.
+ </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>