In recent years, there have been enormous investments in complete genome sequencing of species that fall close to one another on the tree of life, to permit comparative analyses on unprecedented scales. These analyses depend critically on the existence of rigorous and efficient computational tools. Our PHylogenetic Analysis with Space/Time models (PHAST) software package has developed into one of the most widely used toolsets in comparative genomics. PHAST contains the popular conservation scoring programs phastCons and phyloP, as well as a program for estimating the parameters of rich phylogenetic models, called phyloFit, and numerous supporting programs. We have developed and maintained PHAST for over a decade and it is now used by thousands of genomic researchers. Here we propose to continue our work maintaining, improving, and supporting PHAST, and to make several improvements needed for PHAST to keep abreast of recent developments in the field. Our proposal has two main aims: (1) to continue maintenance of support of PHAST, to make various improvements to our software development process, and to improve the accessibility of the software; and (2) to extend PHAST to support new data sets with hundreds to thousands of genome sequences and richer, more general alignment representations. We will closely coordinate our development of PHAST with the UCSC Genome Bioinformatics group's efforts on alignment, visualization, and genome reconstruction. Our software and browser tracks will remain freely available to the research community.