Ye Cheng

I added the callback as a functor for every individual move found, regardless of their profitability, so tree drifting (accepting certain suboptimal moves) can be implemented. The callback can also...

One limitation of matOptimize is it only works with a particular choice of fitch set among all parsimony optimal assignments -- the fitch set has to be the most common...

~~Under the condition of binary tree and unweighted parsimony, the previous comment summarizes to "find_profitable_moves" and "individual_move" assume their input tree has optimally assigned ancestral sequences.~~ ~~When there are polytomies,...

Sorry, I have some difficulties reproducing it. I tried to build it from the source on the master branch or via the public container, and it seems to be working....