PSPE (Phylogenetic Simulation of Promoter Evolution) is a computational tool specifically designed for simulating evolution of non-coding DNA sequences, in particular promoter sequences.
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Weichun Huang, Joseph R Nevins, and Uwe Ohler,
Phylogenetic simulation of promoter evolution: estimation and modelling of binding site turnover events and assessing their impact on alignment tools,
Genome Biology, Vol 8 (10) 2007