The newest releases of the workflow and WebApp now allow for final results without the need for transcriptomic data for all species during the workflow steps. Nevertheless, if possible the workflow should be run with input RNA-Seq reads (both PE/SE possible) suitable for differential expression experiments (control vs. treatment), either a genomic or transcriptomic fasta file + annotation (.gtf) as well as a peptide fasta per species. This way, valuable phylogenetic information from species without available expression information for the conditions under investigation can be included.