  Phylogenetic reconstruction aims at finding plausible hypotheses of the
evolutionary history of genes or species based on genomic sequence information.
The distinction of orthologous genes (genes that having a common ancestry and
diverged after a speciation) is crucial and lies at the heart of many genomic
studies. However, existing methods that rely only on 1:1 orthologs to infer
species trees are strongly restricted to a small set of allowed genes that
provide information about the species tree. The use of larger gene sets that
consist in addition of non-orthologous genes (e.g. so-called paralogous or
xenologous genes) considerably increases the information about the evolutionary
history of the respective species. In this work, we introduce a novel method to
compute species phylogenies based on sequence data including orthologs,
paralogs or even xenologs.
