How to resolve polytomies, rearrange and reconcile a gene tree with species tree using NOTUNG
I am using NOTUNG from the command line for reconciliation of my gene tree with species tree. However, the tree is full of polytomies. It was generated using MrBayes. I don't understand if I should use --resolve --rearrange --reconcile all three options together for reconciliation? What is the difference between only reconciling or rearranging, I see that the output is more or less the same? I find it very confusing, what is the standard process to follow and how sure I can be that the duplications and losses predicted are indeed correct?
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