Effects of the number of aligned mammalian species on the TFBS detection accuracy. Each panel shows the performance of a tool in aligning a different number of species. Human and baboon were used for the two species alignment, mouse was added for the three species alignment, and all five species but cow were used for four species alignment. While all tools have almost the same performance for aligning the two closely related species human and baboon, MUSCLE and DIALIGN performed better than other tools in maintaining or improving performance when adding more species to the alignment.
Huang et al. Genome Biology 2007 8:R225 doi:10.1186/gb-2007-8-10-r225