From 7723baa88fa4f365c01e9f0ee9551e278219d2e5 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 17 Nov 2022 09:39:38 +0000
Subject: [PATCH] JAL-4019 Clarification of position on 'X' in help text

---
 help/help/html/colourSchemes/index.html               |    2 +-
 help/help/html/colourSchemes/nucleotideambiguity.html |    5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html
index 3b16d41..9ba0578 100755
--- a/help/help/html/colourSchemes/index.html
+++ b/help/help/html/colourSchemes/index.html
@@ -459,7 +459,7 @@ td {
 							<td>I</td>
 							<!--Inosine-->
 							<td>X</td>
-							<!--Xanthine (sometimes Unknown)-->
+							<!--Unknown (sometimes Xanthine)-->
 							<td>R</td>
 							<!--Unknown Purine-->
 							<td>Y</td>
diff --git a/help/help/html/colourSchemes/nucleotideambiguity.html b/help/help/html/colourSchemes/nucleotideambiguity.html
index bf097cd..c1ab548 100755
--- a/help/help/html/colourSchemes/nucleotideambiguity.html
+++ b/help/help/html/colourSchemes/nucleotideambiguity.html
@@ -39,6 +39,9 @@ td {
   <p>
   This colour scheme was devised by Suzanne Duce and the Jalview Team to highlight ambiguity codes used in nucleotide sequences.
   </p>  
+  <p>
+  The use of X to represent an unknown base is acknowledged, but this is not recommended as the symbol refers to xanthine (see IUPAC-IUB Commission on Biochemical Nomenclature (CBN). <a href="https://iupac.qmul.ac.uk/misc/naabb.html">Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents.</a>)
+  </p>
   <div align="center">
     <table width="200" border="1">
       <tr>
@@ -67,7 +70,7 @@ td {
       </tr>
       <tr>
         <td bgcolor="#4f6f6f">X</td>
-        <td>Xanthine (sometimes Unknown)</td>
+        <td>Unknown (sometimes Xanthine)</td>
       </tr>
       <tr>
         <td bgcolor="#CD5C5C">R</td>
-- 
1.7.10.2