**2.1.6 Results output**

The output of the search algorithm is the exon-intron structure of all identified tandem gene duplications combined in one result, and the exon-intron structure of each duplicated gene alone. For every result a gene structure drawing is shown, as well as several options to further examine gene details like the alignment of the query sequence to the translation of the hit and the hit itself (Fig. 2).

## **2.2 WebScipio integration**

The search algorithm is fully integrated into the web interface of WebScipio. The search for tandem gene duplications can be enabled in the Advanced Options section. WebScipio provides an interface to easily set the parameters, suggests default parameters, which will be suitable for most cases, and offers documentation at several help pages and examples. The raw results for the gene cluster can be downloaded all together in one YAML file or the result for each gene of the cluster in a separate file. In addition to the raw data, the SVG figures of the gene structures and FASTA files of the sequences (cDNA, genomic DNA, exons, introns, target translation) are available for download. WebScipio provides an upload option for downloaded YAML files to let the user analyse his results at a later date.
