Citation

If you publish research that uses iq-tree you have to cite it as follows:

To cite IQ-TREE please use: - Lam Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32, 268-274. http://doi.org/10.1093/molbev/msu300

To cite the ultrafast bootstrap (UFBoot) please use: - Bui Quang Minh, Minh Anh Thi Nguyen, and Arndt von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol., 30:1188-1195. http://doi.org/10.1093/molbev/mst024

IQ-TREE can use PLL for likelihood computations, if you use "-pll" option please cite: - T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L.-T. Nguyen, B.Q. Minh, A. von Haeseler, and A. Stamatakis (2014) The phylogenetic likelihood library. Syst. Biol., in press. http://doi.org/10.1093/sysbio/syu084