I've used OMA 2.2.0 standalone to generate an estimated species tree from 34 genomes. The tree was successfully generated but I can't seem to find any explanations for the numbers on the tree. Are the node numbers the bootstrap values? Levels of similarity? And the scale bar? Is that a reflection of site substitutions? Difference between HOGs of some sort? I'm so sorry if this is a fundamental question but my googling has failed me.
Thanks in advance for anyone out there that could help me out! :)