Dear Giacomo, (sorry for misspelling your name!)
I had a look at the code. The EVAL mode does not do what it's supposed to do. But there is an undocumented mode (RECONCILE instead of EVAL) that does. Here is the current state:
- EVAL does not optimize anything. It uses default DTL rates (0,2 for each) and only computes the reconciliations.
- RECONCILE does not optimize the gene trees, but it optimizes the DTL rates. If you use --per-family-rates, the per-family rates and reconciliation likelihood scores are outputed in the stats files.
In both mode, the total reconciliation likelihood in the logs is wrong (we always prints 0). I have fixed this in the last commit, but it's only available from GitHub (not in BioConda).
Let me know if that's enough for your purpose. I hope this will be fast enough, because the RECONCILE mode that estimates the DTL rates should be slower than the EVAL mode that only computes the reconciliations...
I plan to rewrite this poorly written part of the code from scratch and to update the documentation in the next days. I am sorry for the mess...
One last observation: if your gene trees were inferred from the sequences only, and not corrected with GeneRax (nor with any other species tree aware method), the DTL rates are very likely to be substantially overestimated. I often observed that GeneRax and all existing reconciliation software tend to compensate gene tree reconstruction error with transfers or DL events.
Best,
Benoit