From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 17 Sep 2024 16:05:09 +0000 (+0100)
Subject: JAL-4418 documentation for 4461
X-Git-Tag: Release_2_11_4_0~4^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d94e2889036b7ea99c36045cc6d73c4f497139a5;p=jalview.git

JAL-4418 documentation for 4461
---

diff --git a/help/help/html/io/index.html b/help/help/html/io/index.html
index b0d6b04..9fb9430 100755
--- a/help/help/html/io/index.html
+++ b/help/help/html/io/index.html
@@ -75,6 +75,10 @@
     <em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file,
       NBRF/PIR, Pfam/Stockholm</em>
   </p>
+  <p><em>By Extension</em> - when this format option is selected, 
+  jalview will automatically determine the format by the .extension 
+  in the filename.</p>
+  <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 &quot;Output&quot;
@@ -84,6 +88,7 @@
   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>
   <p>
     Quantitative and symbolic <a href="../features/annotation.html">alignment
       annotation</a> can be exported as a comma separated value file by
@@ -94,7 +99,7 @@
     annotations and trees in a Jalview archive file using <strong>Desktop&#8594;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).
+    and Varna), PCA and PaSiMap plots, and Trees.
   </p>
   <p>&nbsp;</p>
 </body>