Multiple sequence alignment is a basic
bioinformatics task with many downstream
applications, including phylogeny estimation.
In this talk I will describe two methods we have
developed to improve multiple sequence alignment,
including PASTA (the successor to SATé) and
UPP. Both methods are able to
align ultra-large datasets with up to 1,000,000
sequences with high accuracy, and do so very quickly.
PASTA and UPP are both joint work with my former students Siavash Mirarab and Nam-phuong Nguyen.