The PHylogenetic Analysis with Space/Time models (PHAST) software package consists of a collection of command-line programs and supporting libraries for comparative genomics. PHAST is best known as the engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser. However, it also includes several other tools for phylogenetic modeling and functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations. PHAST has been in development since 2002 and has now been downloaded more than 1000 times, but so far it has been released only as provisional ('beta') software. Here, we describe the first official release (v1.0) of PHAST, with improved stability, portability and documentation and several new features. We outline the components of the package and detail recent improvements. In addition, we introduce a new interface to the PHAST libraries from the R statistical computing environment, called RPHAST, and illustrate its use in a series of vignettes. We demonstrate that RPHAST can be particularly useful in applications involving both large-scale phylogenomics and complex statistical analyses. The R interface also makes the PHAST libraries acccessible to non-C programmers, and is useful for rapid prototyping. PHAST v1.0 and RPHAST v1.0 are available for download at http://compgen.bscb.cornell.edu/phast, under the terms of an unrestrictive BSD-style license. RPHAST can also be obtained from the Comprehensive R Archive Network (CRAN; http://cran.r-project.org).