Jeff R. Proctor and Irmtraud M. Meyer. CoFold: an RNA secondary structure prediction method that takes co-transcriptional folding into account. Nucleic Acids Research. (2013) doi:10.1093/nar/gkt174
Used to create arc plots on the CoFold web server
Daniel Lai, Jeff R. Proctor, Jing Yun A. Zhu, and Irmtraud M. Meyer. R-chie: a web server and R package for visualizing RNA secondary structures. Nucleic Acids Research. (2012) doi:10.1093/nar/gks241