If you use CopyCat, please cite the following paper:
Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson, Markus Göker. COPYCAT: Co-phylogenetic Analysis tool. Bioinformatics, 23(7):898-900, 2007. PDF
Users of AxParafit and AxPcoords may also cite:
Alexandros Stamatakis, Alexander F. Auch, Jan P. Meier-Kolthoff, Markus Göker. AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics 8:405, 2007. PDF