Xenacoelomorpha (comprising Xenoturbellida, Acoela and Nemertodermatida) is a clade of marine worms whose position in the tree of life is still in debate. Several phylogenetic analyses have shown them to be placed at the base of all bilaterian animals (e. g. chordates, arthropods) or at a more derived position as sister group to the Ambulacraria (echinoderms and hemichordates) within the Bilateria. A key characteristic is the absence of traits found in other bilaterian animals. Orthogroups are groups of orthologous genes found in several organisms. Orthologues are assumed to retain the same function. These functions would be specific to the clade where an orthogroup is prevalent. I investigate a method to automatically establish and validate orthogroups specific to Bilateria, Protostomia and Deuterostomia. These genes could be relevant for the clades' respective emergence and differences. These sets will also help to ascertain what genes/functions are absent from Xenacoelomorpha. MicroRNAs (miRNAs) are small non-coding RNA molecules involved in RNA silencing and post-transcriptional regulation of gene expression. MiRNAs have not been extens- ively studied in the Xenaceolomorpha. I introduce a fully automatic miRNA detection pipeline to infer and confirm the existence of pre-miRNA sequences in the genome of Xenoturbella bocki as well as predict miRNA candidates from several xenacoel gen- omes. I report previously undetected miRNA families and opine that previous analyses on Acoelomorpha failed due to loss caused by the higher evolutionary rate when compared to the Xenoturbellida.