New help files

[jalview.git] / help / html / io / index.html

diff --git a/help/html/io/index.html b/help/html/io/index.html
index 332cdca..063f329 100755 (executable)
--- a/help/html/io/index.html
+++ b/help/html/io/index.html
@@ -28,6 +28,11 @@ containing the problem file to jalview@jalview.org.
 <p>Each alignment, whether it is the original or an edited version may be saved\r
   in the standard formats using <strong>File&#8594;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 &quot;Output&quot; tab on the Preferences window where you can \r
+select which file formats you want to append the start and end sequence positions \r
+for. \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&#8594;Save project</strong>. </p>\r
 <p>&nbsp;</p>\r