If you use CAPS in your research, please include the following citations:

CAPS: coevolution analysis using protein sequences.
Fares MA, McNally D.
Bioinformatics. 2006 Nov 15;22(22):2821-2.
PMID: 17005535
https://www.ncbi.nlm.nih.gov/pubmed/17005535

The mathematical model has been described separately:
A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.
Fares MA, Travers SA.
Genetics. 2006 May;173(1):9-23.
PMID: 16547113
https://www.ncbi.nlm.nih.gov/pubmed/16547113