Schematic overview of the TRAPID pipeline. The TRAPID pipeline consists of two separate steps. The first one is a non-interactive processing step, during which all transcripts are assigned to gene families using a RAPSearch2 similarity search, followed by functional annotation transfer and meta-annotation assignment. The second step is interactive and directly commanded through the website interface. Here, the user has the ability to analyze his data using functional enrichment analyses, multiple sequence alignments, and phylogenetic trees.