With the publication of the beam search variant of BCD supertrees (Fleischauer and Böcker, PeerJ 2018), this project has come to an end. BCD supertrees shows an outstanding performance for a supertree method with guaranteed polynomial running time, and is usually on par or even better than established supertree methods such as MRP or SuperFine. With the beam search, you can trade running time for supertree quality; but for input trees that contain branch lengths, even the “regular” BCD shows excellent performance.
We sincerely hope that someone will continue our work and, in particular, will integrate BCD supertrees into a divide-and-conquer strategy to improve the quality of phylogenetic reconstruction for very large trees. In (Fleischauer and Böcker, Mol Biol Evol 2017) we have shown that this is indeed possible (Fig. 2): Computation with RAxML gets faster and the tree quality is improved. Given BCDs fast and guaranteed running times, this should be very interesting for large phylogenies with several thousand taxa: BCD requires only hours to compute a supertree with 5000+ taxa and, even more importantly, supertree quality does not deteriorate for such large datasets.
For us, this is it in phylogenetics — at least, for the moment. It has been a great experience with challenging and fascinating combinatorial problems!
ps. We gratefully acknowledge funding by Deutsche Forschungsgemeinschaft.
pps. The BCD code is available on GitHub.