New commands in NIFAS for analyzing orthology. The three checkboxes to the left are for applying cutoffs. If the “collapse” checkbox is marked, all proteins that have an orthology bootstrap support below the cutoff are hidden. The “Orthology” checkbox groups orthologs based on an average-linkage algorithm described in Hollich et al. (2002). If the orthologous groups are ambiguous, “auto adjust” tries to minimize the number of overlapping orthologous groups by going through all cluster cutoffs within the range of the corresponding value, with a mean of the original cutoff. In the box to the middle, the user can choose the HOPS level for which ortholog assignments are shown. Presently these are the eukaryotic and metazoan levels. The checkboxes to the right allow choosing what species of the present level should be included in the clustering.