Analyzing DNA recombination processes is a scientific problem that is both process and data driven. Applying the technique of scientific workflow in this problem was useful and showed the importance of such method. The detection of recombination from DNA sequences is relevant to the understanding of evolutionary and molecular genetics. While programs such as GENECONV have been identified as detecting recombination more reliably than others, previous studies have not analyzed how many

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... ons they fail to detect. We developed a scientific workflow method for simulating recombination and testing the effect of pairwise differences on its detectability. Decreases in recombination rate due to pairwise differences resulted in population clusters analogous to sympatric speciation under specific conditions and decreases in detectability of recombination, the phenomenon of cryptic recombination. Also, this computational method demonstrated the value of scientific workflow methods for analyzing a complex process and data-driven problem.