anchor.diff:              </li>
               <li>
                 A newly developed hybrid strategy,
  -              which combines LCA* and MRTL based on a given scaling factor.
  +              which combines LCA* and MRTL 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>
             </ul>
           </p>
           <p>
  -          Before this aggregation, we combine the results of each reading frame
  -          and paired-end with <code>uniq</code>.
  -        </p>
  -        <pre>
  -<!--   --><b>$</b> umgap uniq < found-kmers.fa | umgap taxa2agg -m tree -a hybrid -f 0.75 taxons.tsv > classification.fa
  +          Before this aggregation, we remove the markers from the headers with <code>sed</code>
  +          and combine the results of each reading frame and paired-end with <code>uniq</code>.
  +        </p>
  +        <pre>
  +<!--   --><b>$</b> sed '/^>/s_/.*__' < found-kmers.fa | umgap uniq | umgap taxa2agg taxons.tsv | tee classification.fa
  +<!--   -->>read1
  +<!--   -->940615
  +<!--   -->>read2
  +<!--   -->392734
  +<!--   -->>read3
  +<!--   -->332163
           </pre>
           <p>
             Finally, the whole sample is summarized using e.g. a frequency table,
  
positive.code:           As this dataset contains paired-end reads in FASTQ format, and UMGAP operates on FASTA data,
            we perform a first preprocessing step to convert the FASTQ into FASTA files.
          </p>
          <pre>
  <!--   --><b>$</b> umgap fastq2fasta A1.fq A2.fq | sed '/^>/s_/[12]$__' > preprocessed.fa
          </pre>
          <p>
            This command will interleave the given FASTQ files and output a FASTA stream,
            in which the paired-ends alternate each other.
            We use a `sed` substitution to remove the "/1" or "/2" indicating the end,
            as we will pool the ends later on anyway.
          </p>
        </div>
      </div>
  
negative.code:           or one of the many visualizations Unipept offers.
          </p>
          <pre>
  <!--   --><b>$</b> grep -v '^>' < classification.fa | umgap report -r species taxons.tsv | tee report.csv
  <!--   -->1,332163,Candidatus Solibacter usitatus
  <!--   -->1,392734,Terriglobus roseus
  <!--   -->1,940615,Granulicella tundricola
          </pre>
          <p>
            The <code>grep</code> command will drop the FASTA 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.
            This command will prove more useful with larger input.
          </p>
        </div>
      </div>
  