User:Matthew Whiteside/Notebook/Ortholuge Development/Tasks/Task5

TASK5: Ortholog groups

Notes

Decision: anything that we would want to combine in a triplet will be found in same cluster group. Now in cluster groups, actual rbb ortholog pairs are recorded, but we still want triplets for every possible combo, which may not have a rbb ortholog relationship (i.e. as long as gene is an rbb ortholog to one member of group, it is added and will be tripletized with all other members of group).

Question: how do i handle the case: gene 1 has two top hits, one of those top hits' is reciprocal the other is not.

To Do List

1. resolve non-transitive groups (i.e. not all orthologs are reciprocally orthologs) - ongoing
2. check out Thea's approach for handling ties - ongoing

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