Together with David Hanson, I developed R package tdllicor which reads TDL and Licor files, aligns them, and calculates quantities of interest with bootstrap intervals. It is currently private as it is specialized and not of general interest. It has already been important for a number of conference publications and is used for active research:
DT Pater, EB Erhardt, and DT Hanson. Photorespiratory and respiratory carbon
isotope fractionation in leaves. In Proceedings of the Biophysical Society 55th
Annual Meeting, Baltimore, MD, Mar 2010. Biophysical Society.
DT Pater, EB Erhardt, and DT Hanson. Isotopic signature of photorespiration.
In Joint Annual Meetings of the American Society of Plant Biologists and the
Canadian Society of Plant Physiologists, Montreal, CA, August 2010.