faffaf6750cf5492f3bd779a8e2d3fe4116e24d6
jnavarr5
  Tue Jul 28 14:53:49 2026 -0700
Documenting the codonTable genomes.txt setting on the trackDb hub settings page and the track hub help page, with the changes page now linking to the new settings entry, refs #16550

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 21ad504243e..bf1f741f3a0 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -700,30 +700,36 @@
 <em id="organism">organism</em> - the string which is displayed along with the description on most title pages
 in the Genome Browser. Adjust your names in organism and description until they are appropriate. This
 organism name is the name that appears in the genome pull-down menu on the browser gateway page.</p>
 <p>
 <em id="scientificName">scientificName</em> - specifies the scientific name for the assembly.</p>
 <p>
 <em id="defaultPos">defaultPos</em> - specifies the default position the genome browser will open when a user first
 views this assembly. This is usually selected to highlight a popular gene or region of interest in
 the genome assembly.</p>
 <p>
 <em id="orderKey">orderKey</em> - used with other genome definitions at this
 hub to order the genome pull-down.</p>
 <p>
 <em id="htmlPath">htmlPath</em> - refers to an html file that is used on the gateway page to display
 information for a novel assembly.</p>
+<p>
+<em id="codonTable">codonTable</em> - an optional setting that assigns
+<a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi" target="_blank">NCBI genetic
+codes</a> (codon translation tables) to individual sequences for amino acid display, for example
+<code>codonTable default=1 NC_017929.1=13</code>; see the assembly hub
+<a href="assemblyHubHelp.html#codonTable">codonTable</a> documentation for details.</p>
 <h6 id="example_genomes.txt">Example genomes.txt including a newOrg1 assembly</h6>
 <pre><code><strong>genome</strong> hg18
 <strong>trackDb</strong> hg18/trackDb.txt
 <br>
 <strong>genome</strong> hg19
 <strong>trackDb</strong> hg19/trackDb.txt
 <br>
 <strong>genome</strong> newOrg1
 <strong>trackDb</strong> newOrg1/trackDb.txt
 <strong>twoBitPath</strong> newOrg1/newOrg1.2bit
 <strong>groups</strong> newOrg1/groups.txt
 <strong>description</strong> Big Foot V4
 <strong>organism</strong> BigFoot
 <strong>defaultPos</strong> chr21:33031596-33033258
 <strong>orderKey</strong> 4800