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How to cite?
To maintain IQ-TREE, support users and secure fundings, it is important for us that you cite the following papers, whenever the corresponding features were applied for your analysis. Note that the paper of Nguyen et al. (2015) only described the tree search algorithm. Thus, it is not enough to only cite this paper if you, for example, use partition models, where Chernomor et al. (2016) should be cited.
General citation for IQ-TREE 2:
B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534. https://doi.org/10.1093/molbev/msaa015
When using concordance factors please cite:
B.Q. Minh, M.W. Hahn, R. Lanfear (2020) New methods to calculate concordance factors for phylogenomic datasets. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msaa106
When using heterotachy models please cite:
S.M. Crotty, B.Q. Minh, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, A. von Haeseler (2020) GHOST: Recovering historical signal from heterotachously-evolved sequence alignments. Syst. Biol., 69:249-264. https://doi.org/10.1093/sysbio/syz051
When using the tests of symmetry please cite:
S. Naser-Khdour, B.Q. Minh, W. Zhang, E.A. Stone, R. Lanfear (2019) The Prevalence and Impact of Model Violations in Phylogenetic Analysis. Genome Biol. Evol., 11:3341-3352. https://doi.org/10.1093/gbe/evz193
When using polymorphism-aware models please cite:
D. Schrempf, B.Q. Minh, A. von Haeseler, C. Kosiol (2019) Polymorphism-aware species trees with advanced mutation models, bootstrap, and rate heterogeneity. Mol. Biol. Evol., 36:1294–1301. https://doi.org/10.1093/molbev/msz043
When performing ultrafast bootstrap (UFBoot) please cite:
D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281
When using posterior mean site frequency model (PMSF) please cite:
H.C. Wang, B.Q. Minh, S. Susko, A.J. Roger (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol., 67:216–235. https://doi.org/10.1093/sysbio/syx068
When using model selection (ModelFinder) please cite:
S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods, 14:587-589. https://doi.org/10.1038/nmeth.4285
When using partition models please cite:
O. Chernomor, A. von Haeseler, B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol., 65:997-1008. https://doi.org/10.1093/sysbio/syw037
When using IQ-TREE web server please cite:
J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.. Nucleic Acids Res., 44:W232-W235. https://doi.org/10.1093/nar/gkw256
For IQ-TREE 1 please cite:
L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.. Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300
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