Orthologous groups generated in this study are provided for download from https://applbio.biologie.uni-frankfurt.de/download/SARS-CoV-2/Proteome. Provided are the files for an interactive inspection of the feature-aware phylogenetic profile of SARS-CoV-2 using PhyloProfile. Before running PhyloProfile, the custom Coronaviridae taxonomic information provided in the supplement within the data directory should replace the files that come with the default installation of PhyloProfile. To do so, please follow the guidelines below
1.	Install Phyloprofile according to the installation requirements and instructions as described in the software’s website (https://github.com/BIONF/PhyloProfile)
2.	Start R and identify the location where the PhyloProfile package was installed by issuing the command find.package(“PhyloProfile”) in the R prompt. We refer to this path now as the $INSTALLATIONPATH
3.	Place the taxonomy files provided with the SARS-CoV-2 data set (https://applbio.biologie.uni-frankfurt.de/download/SARS-CoV-2/taxon_data.zip into the directory $INSTALLATIONPATH/PhyloProfile/data. This can be done with any file browser
4.	Start up PhyloProfile from the R prompt. Once the PhyloProfile web interface appears, you can upload the provided files for visualization
-	Main input file: coronavirus.phyloprofile
-	Additional annotation input: coronavirus.domains
-	Order taxa by user defined tree: coronavirus.nwk
-	FASTA file optional input: coronavirus.fasta
The phylogenetic profile is represented in the main plot. The feature architecture can be inspected for each data point in the detailed view, showing the feature architecture of the protein in SARS-CoV-2 on top, and its respective ortholog at the bottom.

Data S2. SARS-CoV-2 phylogenetic profile of polyprotein components. Orthologous groups for the SARS-CoV-2 P1ab components are provided for download from https://applbio.biologie.uni-frankfurt.de/download/SARS-CoV-2/P1ab