Explore advances in large-scale multiple sequence alignment through this informative conference talk by Tandy Warnow at the Computational Genomics Summer Institute (CGSI) 2023. Delve into cutting-edge techniques and methodologies for improving alignment accuracy and efficiency in genomic research. Learn about innovative approaches such as MAGUS, which utilizes graph clustering for multiple sequence alignment, and WITCH, which employs weighted consensus HMM alignment. Examine the evaluation of statistical multiple sequence alignment methods in comparison to other alignment techniques on protein data sets. Discover insights on phylogeny-aware alignment using BAli-Phy for accurate large-scale phylogenetic analysis. Gain a deeper understanding of the current state and future directions of multiple sequence alignment evaluation in computational biology.