Levels Of Orthology From Trees. Genes in a subsection of the tree for COG4565 (transcription regulatory protein Dpia) have been numbered according their levels of relatedness. The tree has been analyzed for gene duplication (red squares) and speciation events (green circles), after which the numbering scheme ([3.1], [3.1.1] etc.) of LOFT gives a formal description of the levels of relatedness between the genes that allows a multi-level, scalable orthology. Only the part of the tree from COG4565, containing one of its orthologous groups () is shown.