- in the formats</p>\r
-<p><em>Fasta , MSF, Clustal, BLC, PIR, MSP, PFAM </em></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 file can \r
- be easily imported into Microsoft Powerpoint, Microsoft Word or Adobe Illustrator.<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. </p>\r
-<p>The alignment can be printed from a local printer.</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
+Jalview will by default append the sequence start and end to each sequence name, \r
+in the format /start-end. If you do not want this behaviour for a particular file \r
+output, open the "Output" tab on the <a href="../features/preferences.html">Preferences</a> window where you can \r
+select which file formats you want to append the start and end sequence positions \r
+for. In the case of PIR format, the output tab also contains a switch\r
+for turning on the output of Modeller style structured description\r
+lines.\r
+<p>Quantitative and symbolic <a href="../features/annotation.html">alignment annotation</a> can be exported as a\r
+comma separated value file by right clicking on an annotation row\r
+under the alignment.</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