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CisEvolver is a molecular evolution simulation program written in PERL by Daniel Pollard and Alan Moses. CisEvolver was developed for the following two studies:

Pollard, D. A., Moses, A. M., Iyer, V. N., Eisen, M. B., Detecting the Limits of Regulatory Element Conservation and Divergence Estimation Using Pairwise and Multiple Alignments. BMC Bioinformatics, 2006. 7:376.
[Download Provisional PDF (240 Kb)] [BMC Bioinformatics] [PubMed]

Moses, A. M., Pollard, D. A., Nix, D. A., Iyer, V. N., Li, X., Biggin, M. D., Eisen, M. B., Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Computational Biology, In Press.
[Download Provisional PDF (456 Kb)] [PLoS Computational Biology]

CisEvolver can evolve background genomic DNA sequences or a mixture of background genomic DNA sequences and transcription factor binding sites, down a mutation guide tree. CisEvolver produces an alignment of the leaf sequences generated by the simluation. For more information about CisEvolver please refer to the above manuscripts or the README file for the program. For further questions email dpollard-at-berkeley-dot-edu.

CisEvolver version 0.4 is freely available. Download

The README file can be viewed here: README