* 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/>.
---!>
-<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>.</p>
-<p> </p>
-</body>
-</html>
+-->