FunTFBS is a tool used for identifying transcriptional factor binding sites (TFBS) which have transcriptional regulatory functions. According to binding motifs, the sequence affinities of TFs to genome are different among base pairs within binding sites. The mutations in different base pairs have different effects on the binding of TFs and thus the selective constrains are different. So for functional binding sites, the base pairs with higher affinity are more conserved across species than non-functional ones. Hinted by this, FunTFBS was developed to identify functional TFBS based on the correlation between frequencies in binding motifs and conservation scores. Given the genomic position of candidate TFBS, TF binding motif, genome sequence and PhyloP scores, FunTFBS can filter for functional ones based on the correlation between frequencies in binding motif and conservation scores across base pairs.