Abstract: Phylogenies are a fundamental tool that provide insight into microbial dynamics. Yet phylogenies can be very challenging on large biological datasets, especially when attempting to infer species phylogenies from multiple genes. In this talk I will describe some advances in improving phylogenetic tree estimation on large and ultra-large datasets, and then also identify some challenges where new ideas and techniques are needed. Some of this work is joint with my current and former students and postdocs, including Prof. Siavash Mirarab, Prof. Erin Molloy, Dr. Paul Zaharias, Dr. Vladimir Smirnov, Mr. Minhyuk Park, and Ms. Eleanor Wedell.