TFBSTools (an R/bioconductor package for transcription factor binding site analysis) has been published in Bioinformatics. As a successor of our famous TFBS perl module, TFBSTools highly expands the functionality to provide efficient genome-wide analysis of TFBSs, while retaining equivalent class structure where possible. Some highlights include TFBS detection, de novo discovery, pairwise phylogenetic footprinting and matrix profile retrieval from JASPAR data package. The users of TFBS perl module are highly recommended to migrate to TFBSTools for new features and bug fixes.