anchor.diff:            At this step of the pipeline, we have a list of taxon identifiers per protein,
             one protein per reading frame, 6 reading frames per paired-end and 2 paired-ends per metagenomics read.
             To get a single taxon identification per read, we need to aggregate these 12 lists.
  -          UMGAP offers 3 alternative aggregation strategies with varying speciality.
  +          <span class="initialism">UMGAP</span> offers 3 alternative aggregation strategies with varying speciality.
   
             <ul>
               <li>
  -              Unipept's lowest common ancestor strategy (LCA*),
  +              Unipept's lowest common ancestor strategy (<span class="initialism">LCA*</span>),
                 where the consensus taxon is, as before, the taxon of most specific rank
                 which is either descendant or ancestor of every given taxon;
               </li>
               <li>
  -              Kraken's maximum root-to-leaf path (MRTL),
  +              Kraken's maximum root-to-leaf path (<span class="initialism">MRTL</span>),
                 where the consensus taxon is the taxon in the given list
                 which has the most ancestors in the given list;
               </li>
               <li>
                 A newly developed hybrid strategy,
  -              which combines LCA* and MRTL based on a given scaling factor (default 0.25).
  +              which combines <span class="initialism">LCA*</span> and <span class="initialism">MRTL</span> based on a given scaling factor (default 0.25).
                 The hybrid method aims to ignore some outliers without compromising generality.
                 This strategy is the default and will therefore be used below.
               </li>
  
positive.code: <!--   -->>read3/2
  <!--   -->CAAAATGGAGTGGGCGCTACTGCTCCGTGAGCAGGGTCAGTTGGAGGGATTGGGGCGTGCGCTCGGGGATGCTAATGGCGGTGCCCCTGGATTCCTGAGA</pre>
          <p>
            This command will interleave the given FASTQ files and output a FASTA stream,
            in which the paired-ends alternate each other.
          </p>
        </div>
  
negative.code: <!--   -->1,392734,Terriglobus roseus
  <!--   -->1,940615,Granulicella tundricola</pre>
          <p>
            The <code>grep</code> command will drop the <span class="initialism">FASTA</span> headers,
            allowing the <code>report</code> command to snap each taxon to either a species or "unknown"
            and report the frequency table of the results.
          </p>
  