10 months ago by
Disclaimer: I'm one of the developer of OMA standalone. Indeed, lowering the LengthTol parameter might generally link groups together that share only a short common domain. However, there are a few things that you could do:
What type of groups are you looking at. OMA Groups will be generally sparse, but well suited for species tree reconstruction. If this is your goal, because in OMA Groups every protein must be a pairwise ortholog to all its other members, you could probably do lower the threshold without risking too much clustering propagation.
In case you realize that OMA Groups might not be the right type of grouping for your application, check if the protein does not belong to any HOG (Hierarchical orthologous group). If it does, use this type of grouping.
If your Brachyury genome has many fragments, you might also consider renaming it to Brachyury.contig.fa This way, the length criterion is skipped for the genes belonging to Brachyury while still keeping the criterion for the others. You don't need to recompute the AllAll for this.
Hope this might help you. Feel free to get back to us.