has topic Phylogenetic inference Phylogenetic footprinting Comparison of a DNA sequence to orthologous sequences in different species and inference of a phylogenetic tree, in order to identify regulatory elements such as transcription factor binding sites (TFBS). Phylogenetic shadowing is a type of footprinting where many closely related species are used. A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. Phylogenetic shadowing beta12orEarlier Phylogenomics