<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
<p>The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a> of\r
these file formats.</p>\r
-<p>Additionally annotated alignments can be read in from the Jalview format. </p>\r
-<p>Use the "Input Alignment" menu at the top of the main application\r
- window to read in files from </p>\r
+<p>Additionally, annotated whole sets of alignments and trees can be\r
+read from a <a href="../features/jalarchive.html">Jalview (jar)\r
+format</a> file using <strong>Desktop→Load\r
+Project</strong>. </p>\r
+<p>Use the <strong>Desktop→Input Alignment</strong> menu to read in files from:</p>\r
<ul>\r
- <li> the local file system</li>\r
- <li>a website URL</li>\r
- <li>or by copying and pasting into the "Cut & Paste" text window</li>\r
+ <li><strong>From File</strong>: the local file system</li>\r
+ <li><strong>From URL</strong>: the web (please use the full url)</li>\r
+ <li><strong>from Textbox</strong>: a copy and paste into the\r
+ "Cut & Paste" text window</li>\r
</ul>\r
-<p>If a file is of an unknown format or there is any other error reading the alignment\r
- file you will be given an error message, the alignment will not be read in.\r
+<p>Jalview will try to recognise the file type automatically (using\r
+some special <a href="fileformats.html">features</a>). If a\r
+file is of an unknown format or there is any other error reading the\r
+alignment file then you will be given an error message. If you think\r
+Jalview really should be able to read your file, then send an email\r
+containing the problem file to jalview@jalview.org.\r
</p>\r
<p><strong>Output</strong> </p>\r
<p>Each alignment, whether it is the original or an edited version may be saved\r
- in the standard formats</p>\r
+ in the standard formats using <strong>File→Save As</strong></p>\r
<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
-<p>You may save annotated alignments in the Jalview file format. </p>\r
+<p>You can also save the current set of alignments and their colours, annotations and\r
+trees in a Jalview archive file using <strong>Desktop→Save project</strong>. </p>\r
<p> </p>\r
-<p><strong>Export<a name="export"></a></strong></p>\r
-<p>The alignment may also be saved as a HTML web page. </p>\r
-<p>You may save a Portable Networks Graphics (PNG) image of your alignment. </p>\r
-<p>You may save the alignment as an Encapsulated Postscript file. This is a vector\r
- graphics file which may be modified in various graphics applications, such as\r
- Adobe Illustrator.<br>\r
- <br>\r
- Tip: When importing to a Microsoft document, a snapshot image is taken of your\r
- file - this will be blurred. Right-click the image and choose "Edit image."\r
- This will restore the high quality EPS file format output. <br>\r
- NB. Mac OSX users will find that eps files are automatically converted into\r
- PDF files. </p>\r
-<p>The alignment can be printed from a local printer.</p>\r
</body>\r
</html>\r