The --reconcile option does not do anything anymore (but GeneRax won't complain if you use it). It was necessary before because GeneRax did not compute the reconciliations by default. But now, it does. You can now safely remove the "--reconcile" parameter from your command line.
Regarding gene tree ML optimization and DTL rates optimization:
--eval SPR will performs gene tree optimization as well as DTL rates optimization (that's the default parameter)
--eval EVAL won't perform gene tree optimization but will estimate the DTL rates
--eval SKIP won't optimize the gene trees nor the DTL rates (it only makes sense for SpeciesRax users)
In all three cases, GeneRax will reconcile the gene trees with the species tree at the end of the run, unless you set --do-not-reconcile.
If you are unsure, check the logs:
- the ML gene tree optimization will outputs lines like "[00:00:01] Optimizing gene trees with radius=1..."
- the reconciliation is done when you see "[00:00:00] Reconciling gene trees with the species tree..."
And if there is anything unexpected, let me know :)