PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP

Abstract

Summary: The Phylogenetic Analysis with Space/Time models (PHAST) package is a widely used software package for comparative genomics that has been freely available for download since 2002. Here, we introduce a web interface (phastWeb) that makes it possible to use two of the most popular programs in PHAST, phastCons and phyloP, without downloading and installing the PHAST software. This interface allows users to upload a sequence alignment and either upload a corresponding phylogeny or have one estimated from the alignment. After processing, users can visualize alignments and conservation scores as genome browser tracks and download estimated tree models and raw scores for further analysis. Altogether, this resource makes key features of the PHAST package conveniently available to a broad audience.

Availability and implementation: PhastWeb is freely available on the web at http://compgen.cshl.edu/phastweb/. The website provides instructions as well as examples.