anchor.diff:  <!--   --><b>$</b> umgap-visualize.sh -i tryptic-sensitivity-output.fa.gz -w > tryptic-sensitivity.html
   <!--   --><b>$</b> umgap-visualize.sh -i tryptic-sensitivity-output.fa.gz -u
   <!--   --><a href="https://bl.ocks.org/11b7809d6754b9530cf1a49d93a8d568">https://bl.ocks.org/11b7809d6754b9530cf1a49d93a8d568</a></pre>
  +        <p>
  +          The CSV tables contain a record for each taxon found in the sample.
  +          A record contains, in order, the frequency of the taxon, the taxon ID and (for convenience) the taxon name.
  +          All records will be at the same specified taxon rank or at root (unidentified).
  +        </p>
  +        <dl class='dl-horizontal'>
  +          <dt><samp>-i file</samp></dt><dd>Analysis output file, optionally compressed.</dd>
  +          <dt><samp>-t</samp></dt><dd>Output a CSV frequency table on species rank.</dd>
  +          <dt><samp>-w</samp></dt><dd>Output an HTML webpage of an interactive visualization.</dd>
  +          <dt><samp>-u</samp></dt><dd>Print a shareable URL to a online interactive visualisation.</dd>
  +          <dt><samp>-r rank</samp></dt><dd>Set the rank for the CSV frequency table (default: species).</dd>
  +        </dl>
         </div>
  -      <dl class='dl-horizontal'>
  -        <dt><samp>-i file</samp></dt><dd>Analysis output file, optionally compressed.</dd>
  -        <dt><samp>-t</samp></dt><dd>Output a CSV frequency table on species rank.</dd>
  -        <dt><samp>-w</samp></dt><dd>Output an HTML webpage of an interactive visualization.</dd>
  -        <dt><samp>-u</samp></dt><dd>Print a shareable URL to a online interactive visualisation.</dd>
  -        <dt><samp>-r rank</samp></dt><dd>Set the rank for the CSV frequency table (default: species).</dd>
  -      </dl>
       </div>
   
       <h2>References</h2>
  
positive.code:       <div class="card-supporting-text">
          <p>
            After analysis, you probably want to view the results.
            While the output format is easily parsed,
             you can also use the visualize script to create importable CSV frequency tables
             and interactive visualisations.
            The interactive visualisations can be stored locally or hosted online.
            The following snippet creates all three in turn.
          </p>
          <pre style="max-height: initial;">
  <!--   --><b>$</b> umgap-visualize.sh -i tryptic-sensitivity-output.fa.gz -t -r phylum
  <!--   -->2	1117	Cyanobacteria
  <!--   -->4	57723	Acidobacteria
  <!--   -->4	201174	Actinobacteria
  
negative.code:            but you can also use it to verify the file locations and download newer versions of the data.
            If you're planning to use the tryptic precision, tryptic sensitivity, high precision or max precision pipelines,
             you'll need to <a href="https://github.com/unipept/FragGeneScanPlusPlus/">install FragGeneScan++</a> first.
            In this casestudy, we will use a tryptic pipeline, so we don't have to download the 9-mer index (~12GiB, rather than ~150GiB).
          </p>
          <p>
            Following code snippet shows the interaction with the setup script.
  