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Update references to ask users to cite
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‎README.md‎

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@@ -62,22 +62,44 @@ For feature requests bug reports please post a topic at
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Citations
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---------
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General citation for IQ-TREE 2:
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General citation for IQ-TREE 3:
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* B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020)
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IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era.
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*Mol. Biol. Evol.*, 37:1530-1534. <https://doi.org/10.1093/molbev/msaa015>
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* T.K.F. Wong, N. Ly-Trong, H. Ren, H. Banos,
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A.J. Roger, E. Susko, C. Bielow, N. De Maio,
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N. Goldman, M.W. Hahn, G. Huttley, R. Lanfear, B.Q. Minh (2025)
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IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models.
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Submitted.
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Moreover, there are other papers associated with notable features in IQ-TREE,
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which are normally mentioned in the corresponding documentation. We ask that you also
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cite these papers, which are important for us to obtain fundings to
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continuously maintain the code of IQ-TREE. These papers are also listed below.
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> **NOTE**: You can also obtain the citations in `.iqtree` output file.
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When using MixtureFinder please cite:
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* H. Ren, T.K.F. Wong, B.Q. Minh, R. Lanfear (2025)
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MixtureFinder: Estimating DNA mixture models for phylogenetic analyses.
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_Mol. Biol. Evol._, 42:msae264. <https://doi.org/10.1093/molbev/msae264>
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When using GTRpmix model please cite:
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* H. Banos, T.K.F. Wong, J. Daneau, E. Susko, B.Q. Minh, R. Lanfear, M.W. Brown, L. Eme, A.J. Roger (2024)
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GTRpmix: A linked general-time reversible model for profile mixture models.
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_Mol. Biol. Evol._, 92:msae174. <https://doi.org/10.1093/molbev/msae174>
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When using CMAPLE please cite:
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* N. Ly-Trong, C. Bielow, N. De Maio, B.Q. Minh (2024)
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CMAPLE: Efficient phylogenetic inference in the pandemic era.
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_Mol. Biol. Evol._, 41:msae134. <https://doi.org/10.1093/molbev/msae134>
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When using tree mixture models (MAST) please cite:
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* T.K.F. Wong, C. Cherryh, A.G. Rodrigo, M.W. Hahn, B.Q. Minh, R. Lanfear (2024)
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MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.
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_Syst. Biol._, in press. <https://doi.org/10.1093/sysbio/syae008>
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_Syst. Biol._, 73:375–391. <https://doi.org/10.1093/sysbio/syae008>
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When computing concordance factors please cite:
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@@ -89,7 +111,7 @@ When using AliSim to simulate alignments please cite:
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* N. Ly-Trong, G.M.J. Barca, B.Q. Minh (2023)
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AliSim-HPC: parallel sequence simulator for phylogenetics.
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*Bioinformatics*, 39:btad540. <https://doi.org/10.1093/bioinformatics/btad540>
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_Bioinformatics_, 39:btad540. <https://doi.org/10.1093/bioinformatics/btad540>
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When estimating amino-acid Q matrix please cite:
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@@ -152,6 +174,13 @@ When using IQ-TREE version 1 please cite:
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies.
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_Mol. Biol. and Evol._, 32:268-274. <https://doi.org/10.1093/molbev/msu300>
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When using IQ-TREE version 2 please cite:
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* B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020)
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IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era.
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*Mol. Biol. Evol.*, 37:1530-1534. <https://doi.org/10.1093/molbev/msaa015>
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#### Credits and Acknowledgements
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Some parts of the code were taken from the following packages/libraries: [Phylogenetic likelihood library](http://www.libpll.org), [TREE-PUZZLE](http://www.tree-puzzle.de),

‎main/phyloanalysis.cpp‎

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@@ -83,14 +83,113 @@ extern "C" {
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void reportReferences(Params &params, ofstream &out) {
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out << "To cite IQ-TREE please use:" << endl << endl
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<< "Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf," << endl
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<< "Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020)" << endl
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<< "IQ-TREE 2: New models and efficient methods for phylogenetic inference" << endl
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<< "in the genomic era. Mol. Biol. Evol., in press." << endl
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<< "https://doi.org/10.1093/molbev/msaa015" << endl << endl;
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out << "To cite IQ-TREE 3 please use:" << endl << endl
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<< "Thomas K.F. Wong, Nhan Ly-Trong, Huaiyan Ren, Hector Banos, Andrew J. Roger," << endl
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<< "Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W. Hahn," << endl
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<< "Gavin Huttley, Robert Lanfear, Bui Quang Minh (2025)" << endl
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<< "IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models." << endl
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<< "Submitted." << endl << endl;
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out << "Please also cite the following paper(s) for the feature(s) that you used:" << endl << endl;
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bool modelfinder_only = false;
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if (params.model_name.find("MIX") != string::npos && params.model_name.find("MIX{") == string::npos) {
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out << "To cite MixtureFinder please use: " << endl << endl
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<< "Huaiyan Ren, Thomas KF Wong, Bui Quang Minh, Robert Lanfear (2025)" << endl
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<< "MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses." << endl
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<< "Molecular Biology and Evolution, 42:msae264." << endl
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<< "https://doi.org/10.1093/molbev/msae264" << endl << endl;
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}
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if (params.optimize_linked_gtr) {
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out << "To cite GTRpmix please use: " << endl << endl
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<< "Hector Banos, Thomas KF Wong, Justin Daneau, Edward Susko, Bui Quang Minh," << endl
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<< "Robert Lanfear, Matthew W Brown, Laura Eme, Andrew J Roger (2025)" << endl
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<< "GTRpmix: A linked general-time reversible model for profile mixture models." << endl
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<< "Molecular Biology and Evolution, 92:msae174." << endl
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<< "https://doi.org/10.1093/molbev/msae174" << endl << endl;
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}
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if (params.inference_alg != ALG_IQ_TREE) {
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out << "To cite CMAPLE please use: " << endl << endl
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<< "Nhan Ly-Trong, Chris Bielow, Nicola De Maio, Bui Quang Minh (2024)" << endl
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<< "CMAPLE: Efficient phylogenetic inference in the pandemic era." << endl
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<< "Molecular Biology and Evolution, 41:msae134." << endl
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<< "https://doi.org/10.1093/molbev/msae134" << endl << endl;
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}
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if (params.model_name.find("+T") != string::npos) {
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out << "To cite the MAST model \"+T\" please use: " << endl << endl
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<< "Thomas KF Wong, Caitlin Cherryh, Allen G Rodrigo, Matthew W Hahn, Bui Quang Minh, Robert Lanfear (2024)" << endl
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<< "MAST: Phylogenetic Inference with Mixtures Across Sites and Trees." << endl
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<< "Systematic Biology, 73:375–391." << endl
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<< "https://doi.org/10.1093/sysbio/syae008" << endl << endl;
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}
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if (params.consensus_type == CT_ASSIGN_SUPPORT_EXTENDED) {
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out << "To cite site/gene concordance factor please use: " << endl << endl
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<< "Yu K Mo, Robert Lanfear, Matthew W Hahn, Bui Quang Minh (2023)" << endl
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<< "Updated site concordance factors minimize effects of homoplasy and taxon sampling." << endl
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<< "Bioinformatics, 39:btac741." << endl
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<< "https://doi.org/10.1093/bioinformatics/btac741" << endl << endl;
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}
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if (params.alisim_active) {
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out << "To cite AliSim please use: " << endl << endl
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<< "Nhan Ly-Trong, Giuseppe MJ Barca, Bui Quang Minh (2023)" << endl
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<< "AliSim-HPC: parallel sequence simulator for phylogenetics." << endl
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<< "Bioinformatics, 39:btad540." << endl
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<< "https://doi.org/10.1093/bioinformatics/btad540" << endl << endl;
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}
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if (params.model_joint != "" && params.model_joint.find("NONREV") == string::npos) {
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out << "To cite QMaker for estimating protein Q matrix please use: " << endl << endl
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<< "Bui Quang Minh, Cuong Cao Dang, Le Sy Vinh, Robert Lanfear (2021)" << endl
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<< "QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution." << endl
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<< "Systematic Biology, 70:1046–1060." << endl
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<< "https://doi.org/10.1093/sysbio/syab010" << endl << endl;
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}
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if (params.model_joint != "" && params.model_joint.find("NONREV") != string::npos) {
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out << "To cite nQMaker for estimating non-reversible Q matrix please use: " << endl << endl
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<< "Cuong Cao Dang, Bui Quang Minh, Hanon McShea, Joanna Masel, Jennifer E James, Le Sy Vinh, Robert Lanfear (2022)" << endl
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<< "nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models." << endl
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<< "Systematic Biology, 71:1110–1123." << endl
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<< "https://doi.org/10.1093/sysbio/syac007" << endl << endl;
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}
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if (params.consensus_type == CT_ROOTSTRAP) {
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out << "To cite Rootstrap please use: " << endl << endl
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<< "Suha Naser-Khdour, Bui Quang Minh, Robert Lanfear (2022)" << endl
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<< "Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals." << endl
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<< "Systematic Biology, 71:959–972." << endl
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<< "https://doi.org/10.1093/sysbio/syab067" << endl << endl;
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}
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if (params.model_name.find("+H") != string::npos) {
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out << "To cite the GHOST \"+H\" please use: " << endl << endl
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<< "Stephen M Crotty, Bui Quang Minh, Nigel G Bean, Barbara R Holland, Jonathan Tuke, Lars S Jermiin, Arndt Von Haeseler (2020)" << endl
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<< "GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments." << endl
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<< "Systematic Biology, 69:249-264." << endl
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<< "https://doi.org/10.1093/sysbio/syz051" << endl << endl;
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}
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if (params.symtest != SYMTEST_NONE) {
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out << "To cite tests of symmetry please use: " << endl << endl
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<< "Suha Naser-Khdour, Bui Quang Minh, Wenqi Zhang, Eric A Stone, Robert Lanfear (2024)" << endl
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<< "The Prevalence and Impact of Model Violations in Phylogenetic Analysis." << endl
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<< "Genome Biology and Evolution, 11:3341-3352." << endl
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<< "https://doi.org/10.1093/gbe/evz193" << endl << endl;
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}
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// if (DecentTree) {
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// out << "To cite WHAT please use: " << endl << endl
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// << "Weiwen Wang, James Barbetti, Thomas Wong, Bryan Thornlow, Russ Corbett-Detig, Yatish Turakhia, Robert Lanfear, Bui Quang Minh (2023)" << endl
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// << "DecentTree: scalable Neighbour-Joining for the genomic era." << endl
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// << "Bioinformatics, 39:btad536." << endl
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// << "https://doi.org/10.1093/bioinformatics/btad536" << endl << endl;
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// }
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if (params.model_name.substr(0,4) == "TEST" || params.model_name.substr(0, 2) == "MF" || params.model_name.empty()) {
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out << "To cite ModelFinder please use: " << endl << endl
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<< "Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler," << endl
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}
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if (posPOMO(params.model_name) != string::npos) {
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out << "For polymorphism-aware models please cite:" << endl << endl
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<< "Dominik Schrempf, Bui Quang Minh, Nicola De Maio, Arndt von Haeseler, and Carolin Kosiol" << endl
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<< "(2016) Reversible polymorphism-aware phylogenetic models and their application to" << endl
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<< "tree inference. J. Theor. Biol., 407:362–370." << endl
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<< "https://doi.org/10.1016/j.jtbi.2016.07.042" << endl << endl;
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<< "Dominik Schrempf, Bui Quang Minh, Arndt von Haeseler, Carolin Kosiol (2019)" << endl
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<< "Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity" << endl
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<< "Molecular Biology and Evolution, 36:1294–1301." << endl
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<< "https://doi.org/10.1093/molbev/msz043" << endl << endl;
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}
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if (params.site_freq_file || params.tree_freq_file)

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