Orthology groups correspond to HOGs?

[alexvasilikop]

Hello,

Thanks for developing such useful tools. I want to use AGORA with providing the orthologous groups files and not the trees; I have a question regarding these orthology groups. I used Orthofinder for inferring these groups which outputs hierarchical orthogroups (HOGs). For a deep node in the tree the HOGS might only contain a few or even a couple of species. Basically a HOG for a shallow node (e.g. consisting of 2 species) is also a HOG for a deep node (as this shallow node is a child of the deeper node). Should all these groups be provided to all the levels to which they are relevant? Or how do you define the orthologous groups for each node in the species tree, given that some HOGs do not contain all children species of that node?

Thanks Alex