Orthology groups correspond to HOGs? about agora

[alouis72]

Hi Alex,
sorry for the late answer.
I'm not sure I understand your question. All HOGs should be provide according to the species tree.
If you used OrthoFinder to define HOGs, you could be able to run agora with the species tree provided in the Orthofinder results:

Results_XXXX/Phylogenetic_Hierarchical_Orthogroups/
You will have to use the species tree produced by orthofinder for AGORA that should be :
Results_XXXX/Species_Tree/SpeciesTree_rooted_node_labels.txt

After that, to simplify treatment you can use a script available here:
https://github.com/DyogenIBENS/Agora/tree/dev/src/import/orthofinder_hogs/convert_hogs_sp.py
that will format HOGs for AGORA

ex:
python ./convert_hogs_sp.py -of_hogs Results_XXXX/Phylogenetic_Hierarchical_Orthogroups -outdir Agora_data/orthoGroups/

Hope this helps,
Alexandra

[sunriseTM]

I have the same confusion. If a orthogroup only contain 2 genes from a single species, I noticed Agora will construct a ancesral gene corresponding to the two genes, but the ancestor contain many descedents and only this species contain this 2 genes. As I expected, the 2 genes in the orthogroup is species-specific and tend to be new genes, why Agroa construct a ancestral gene based on them?