The executable version of the method implementing the gap-term extension proposed in the paper (gplmDCA) can be downloaded here, while the method implementing modified scoring (plmDCA20) can be downloaded either here or from the main plmDCA website.

If you use gplmDCA (or parts of it), please be sure to cite:
Feinauer C, Skwark MJ, Pagnani A, Aurell E (2014) Improving Contact Prediction along Three Dimensions. PLoS Comput Biol 10(10): e1003847. 
doi: 10.1371/journal.pcbi.1003847