creto (Cis-Regulatory Element Turn-Over) is a program for the determination of the evolutionary origination and decay rates of transcription factor binding sites. Given a phylogenetic tree and the binding site numbers of the species at the tips, creto uses a maximum likelihood model that permits variable turnover rates in different parts of the species tree. This model can be used to detect changes in turnover rate as a proxy for differences in the selective pressures acting on TFBS in different clades.
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Otto W, Stadler PF, Lopez-Gialdez F, Townsend JP, Lynch VJ, Wagner GP
Measuring Transcription Factor Binding Site Turnover: A Maximum Likelihood Approach using Phylogenies.
Genome Biol Evol. 2009 May 25;1:85-98.