A program written in C to compute the nesting index of double occurrence words. Double occurrence words are used to model the recombination of DNA in certain ciliate species. The primary reference/documentation related to this work is my research publication and Master's thesis that you can find here and here, respectively. An introduction to the topic of double occurence words / assembly graphs and their use to model DNA recombination in ciliate species can be found here. For more general information you can visit the research group's web page which is still active at http://knot.math.usf.edu.
Be warned: This is an old project with little or no upkeep.
This program was developed as part of a research project at the University of South Florida with help from advisors Natasha Jonoska and Masahico Saito. The project was supported in part by NSF grant DMS-0900671 and NIH grant 1R01GM109459-01.