Abstract: Large multiple sequence alignments and trees are beneficial for many downstream applications, including the inference of the tree of life, taxonomic abundance profiling of microbiomes, etc.  Because accurate estimation of large alignments and trees can be computationally challenging, one approach to each of these problems is to add the sequences into the alignment or tree.  Doing this with high accuracy is, however, a challenge.  In this talk, I will present methods that have high accuracy for each of these problems.  For adding sequences into alignments, I will discuss UPP, WITCH, and EMMA.  For adding sequences into trees (i.e., phylogenetic placement), I will present SCAMPP and BSCAMPP, two new methods for improving the scalability of maximum likelihood-based placement.  I will also present results showing the impact of these methods in taxonomic abundance profiling for microbiome analysis (e.g., TIPP3).