1a59b509cebd53b0e7f2d322fd0fb46586f53840
lrnassar
  Fri Jul 19 18:38:05 2024 -0700
Restructuring some of the menus based on feedback, refs #33509

diff --git src/hg/htdocs/util.html src/hg/htdocs/util.html
index 5f1ca07..c9bdc7b 100755
--- src/hg/htdocs/util.html
+++ src/hg/htdocs/util.html
@@ -13,31 +13,40 @@
 <a href="../cgi-bin/hgTables">Table Browser</a>, and <a href="../cgi-bin/hgLiftOver">LiftOver</a>.
 We maintain the following less-used tools: <a href="../cgi-bin/hgNear">Gene Sorter</a>,
 <a href="../cgi-bin/hgGenome">Genome Graphs</a>, and
 <a href="../cgi-bin/hgIntegrator">Data Integrator</a>.
 These are available from the &quot;Tools&quot; dropdown menu at the top of the site.</p>
 
 <p>
 We also offer command-line utilities for many file conversions and basic bioinformatics functions.
 You can learn more and download these utilities through the 
 <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">utilities section</a>
 of our downloads page.</p>
 
 <p>
 The following tools and utilities created by the UCSC Genome Browser Group are also available 
 for public use:</p>
-<ul class="gbsNoBullet">
+<ul>
+   <li>
+   <strong><a href="../cgi-bin/hgGenome">Genome Graphs</a></strong> -
+   Allows for the display of any number of annotations as genome-wide density graphs. Useful
+   for exploratory data analysis, publication images, and specific data such as linkage studies.</li>
+   <li>
+   <strong><a href="../cgi-bin/hgNear">Gene Sorter</a></strong> -
+   Displays a sorted table of genes that are related to one another. The relationship can be one 
+   of several types, including protein-level homology, similarity of gene expression profiles, 
+   or genomic proximity.</li>
    <li>
    <strong><a href="../cgi-bin/hgPhyloPlace">UShER</a> (for SARS-CoV-2 only)</strong> - 
    allows placement of SARS-CoV-2 sequences onto existing phylogenetic trees for tracing strains
    and transmission events.</li>
    <li>
    <strong><a title="Explore gene/protein interactions and pathways" 
    href="../cgi-bin/hgGeneGraph">Gene Interactions</a></strong> - 
    displays a gene interaction and pathway graph based on data from curated protein-interaction 
    databases and text mining of PubMed abstracts.</li>   
    <li>
    <strong><a id="visiGeneMenuLink" href="../cgi-bin/hgVisiGene">VisiGene</a></strong> -
    displays high-quality images of in-situ mouse and frogs with gene mRNA hybridization 
    probes and transcription factors.</li>
    <li>
   <strong><a href="http://users.soe.ucsc.edu/~kent/dnaDust/dnadust.html">DNA Duster</a></strong> - 
@@ -50,31 +59,31 @@
   <li>
   <strong><a href="cgi-bin/phyloPng">Phylogenetic Tree PNG Maker</a></strong> - creates a PNG image 
   from phylogenetic tree specification given; several configuration options for branch 
   lengths, normalized lengths, branch labels, legend, etc.</li>
   <li>
   <strong><a href="http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads">Executable and 
   Source Code Downloads</a></strong> - executable and source code downloads of the Genome Browser, 
   Blat and liftOver.</li>
 </ul>
 </p>
 <p>
 The following tools and utilities created by outside groups may be helpful when working with our
 file formats and the genome annotation databases that we provide. References to these tools are
 provided for the benefit of our users. We are unable to support the use of externally developed
 tools; if you have questions or problems, please contact the developers of the tool directly.
-<ul class="gbsNoBullet">
+<ul>
   <li><strong><a href="https://bedops.readthedocs.io/en/latest/">BEDOPS</a></strong> -
       A highly scalable and easily-parallelizable genome analysis toolkit
   </li>
   <li><strong><a href="https://bedtools.readthedocs.io/en/latest/">bedtools</a></strong> -
       A swiss-army knife of tools for a wide-range of genomics analysis tasks
   </li>
   <li><strong><a href="https://github.com/CRG-Barcelona/bwtool/wiki">bwtool</a></strong> -
       A command-line utility for bigWig files
   </li>
   <li><strong><a href="http://crossmap.sourceforge.net/">CrossMap</a></strong> -
       A program for genome coordinate conversion between different assemblies
   </li>
   <li><strong><a href="https://pypi.org/project/cruzdb/">CruzDb</a></strong> -
       Python package to load genome annotations from our servers
   </li>