A lot of discrete tree operations (IC/TC scores, tree plausibility analysis) and some new stuff (quartets and this paper here http://www.biorxiv.org/content/biorxiv/early/2017/06/23/154542.full.pdf) should not go into raxml-ng but rather to the modules. We need to discuss this at some point, but I think all operations on a discrete set of trees that don't require likelihood calculations should not be part of RAxML-NG.
A lot of discrete tree operations (IC/TC scores, tree plausibility analysis) and some new stuff (quartets and this paper here http://www.biorxiv.org/content/biorxiv/early/2017/06/23/154542.full.pdf) should not go into raxml-ng but rather to the modules. We need to discuss this at some point, but I think all operations on a discrete set of trees that don't require likelihood calculations should not be part of RAxML-NG.