These are Python scripts plus C/C++ programs for automating the reference free genomic analysis described in:
Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11).
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995
Analytical concept conceived by CHCannon and CSKua. Original script written in Mathematica by CHCannon.