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add citations for mcmctree and robust phylogenetics
1 parent d89ce07 commit 9303377

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‎main/phyloanalysis.cpp‎

Lines changed: 37 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -90,19 +90,34 @@ void reportReferences(Params &params, ofstream &out) {
9090
<< "IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models." << endl
9191
<< "Submitted." << endl << endl;
9292

93-
out << "Please also cite the following paper(s) for the feature(s) that you used:" << endl << endl;
93+
if (params.dating_method == "mcmctree") {
94+
out << "Since you used IQ2MC dating method please also cite: " << endl << endl
95+
<< "Piyumal Demotte, Muthukumaran Panchaksaram, Hashara Kumarasinghe," << endl
96+
<< "Nhan Ly-Trong, Mario dos Reis, Bui Quang Minh (2025)" << endl
97+
<< "IQ2MC: A New Framework to Infer Phylogenetic Time Trees" << endl
98+
<< "Using IQ-TREE 3 and MCMCTree with Mixture Models." << endl
99+
<< "https://doi.org/10.32942/X2CD2X" << endl << endl;
100+
}
101+
102+
if (params.robust_phy_keep < 1.0) {
103+
out << "Since you used trimed log-likelihood method please also cite: " << endl << endl
104+
<< "Qin Liu, Bui Quang Minh, Robert Lanfear, Michael A. Charleston," << endl
105+
<< "Shane A. Richards, Barbara R. Holland (2025)" << endl
106+
<< "Robust Phylogenetics." << endl
107+
<< "https://doi.org/10.1101/2025.04.01.646540" << endl << endl;
108+
}
94109

95110
bool modelfinder_only = false;
96111
if (params.model_name.find("MIX") != string::npos && params.model_name.find("MIX{") == string::npos) {
97-
out << "To cite MixtureFinder please use: " << endl << endl
112+
out << "Since you used MixtureFinder please also cite: " << endl << endl
98113
<< "Huaiyan Ren, Thomas KF Wong, Bui Quang Minh, Robert Lanfear (2025)" << endl
99114
<< "MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses." << endl
100115
<< "Molecular Biology and Evolution, 42:msae264." << endl
101116
<< "https://doi.org/10.1093/molbev/msae264" << endl << endl;
102117
}
103118

104119
if (params.optimize_linked_gtr) {
105-
out << "To cite GTRpmix please use: " << endl << endl
120+
out << "Since you used GTRpmix please also cite: " << endl << endl
106121
<< "Hector Banos, Thomas KF Wong, Justin Daneau, Edward Susko, Bui Quang Minh," << endl
107122
<< "Robert Lanfear, Matthew W Brown, Laura Eme, Andrew J Roger (2025)" << endl
108123
<< "GTRpmix: A linked general-time reversible model for profile mixture models." << endl
@@ -111,71 +126,75 @@ void reportReferences(Params &params, ofstream &out) {
111126
}
112127

113128
if (params.inference_alg != ALG_IQ_TREE) {
114-
out << "To cite CMAPLE please use: " << endl << endl
129+
out << "Since you used CMAPLE please also cite: " << endl << endl
115130
<< "Nhan Ly-Trong, Chris Bielow, Nicola De Maio, Bui Quang Minh (2024)" << endl
116131
<< "CMAPLE: Efficient phylogenetic inference in the pandemic era." << endl
117132
<< "Molecular Biology and Evolution, 41:msae134." << endl
118133
<< "https://doi.org/10.1093/molbev/msae134" << endl << endl;
119134
}
120135

121136
if (params.model_name.find("+T") != string::npos) {
122-
out << "To cite the MAST model \"+T\" please use: " << endl << endl
123-
<< "Thomas KF Wong, Caitlin Cherryh, Allen G Rodrigo, Matthew W Hahn, Bui Quang Minh, Robert Lanfear (2024)" << endl
137+
out << "Since you used the MAST model \"+T\" please also cite: " << endl << endl
138+
<< "Thomas KF Wong, Caitlin Cherryh, Allen G Rodrigo, Matthew W Hahn," << endl
139+
<< "Bui Quang Minh, Robert Lanfear (2024)" << endl
124140
<< "MAST: Phylogenetic Inference with Mixtures Across Sites and Trees." << endl
125141
<< "Systematic Biology, 73:375–391." << endl
126142
<< "https://doi.org/10.1093/sysbio/syae008" << endl << endl;
127143
}
128144

129145
if (params.consensus_type == CT_ASSIGN_SUPPORT_EXTENDED) {
130-
out << "To cite site/gene concordance factor please use: " << endl << endl
146+
out << "Since you used site/gene concordance factor please also cite: " << endl << endl
131147
<< "Yu K Mo, Robert Lanfear, Matthew W Hahn, Bui Quang Minh (2023)" << endl
132148
<< "Updated site concordance factors minimize effects of homoplasy and taxon sampling." << endl
133149
<< "Bioinformatics, 39:btac741." << endl
134150
<< "https://doi.org/10.1093/bioinformatics/btac741" << endl << endl;
135151
}
136152

137153
if (params.alisim_active) {
138-
out << "To cite AliSim please use: " << endl << endl
154+
out << "Since you used AliSim please also cite: " << endl << endl
139155
<< "Nhan Ly-Trong, Giuseppe MJ Barca, Bui Quang Minh (2023)" << endl
140156
<< "AliSim-HPC: parallel sequence simulator for phylogenetics." << endl
141157
<< "Bioinformatics, 39:btad540." << endl
142158
<< "https://doi.org/10.1093/bioinformatics/btad540" << endl << endl;
143159
}
144160

145161
if (params.model_joint != "" && params.model_joint.find("NONREV") == string::npos) {
146-
out << "To cite QMaker for estimating protein Q matrix please use: " << endl << endl
162+
out << "Since you used QMaker to estimate protein matrix please also cite: " << endl << endl
147163
<< "Bui Quang Minh, Cuong Cao Dang, Le Sy Vinh, Robert Lanfear (2021)" << endl
148164
<< "QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution." << endl
149165
<< "Systematic Biology, 70:1046–1060." << endl
150166
<< "https://doi.org/10.1093/sysbio/syab010" << endl << endl;
151167
}
152168

153169
if (params.model_joint != "" && params.model_joint.find("NONREV") != string::npos) {
154-
out << "To cite nQMaker for estimating non-reversible Q matrix please use: " << endl << endl
155-
<< "Cuong Cao Dang, Bui Quang Minh, Hanon McShea, Joanna Masel, Jennifer E James, Le Sy Vinh, Robert Lanfear (2022)" << endl
170+
out << "Since you used nQMaker to estimate non-reversible Q matrix please also cite: " << endl << endl
171+
<< "Cuong Cao Dang, Bui Quang Minh, Hanon McShea, Joanna Masel," << endl
172+
<< "Jennifer E James, Le Sy Vinh, Robert Lanfear (2022)" << endl
156173
<< "nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models." << endl
157174
<< "Systematic Biology, 71:1110–1123." << endl
158175
<< "https://doi.org/10.1093/sysbio/syac007" << endl << endl;
159176
}
160177

161178
if (params.consensus_type == CT_ROOTSTRAP) {
162-
out << "To cite Rootstrap please use: " << endl << endl
179+
out << "Since you used Rootstrap please also cite: " << endl << endl
163180
<< "Suha Naser-Khdour, Bui Quang Minh, Robert Lanfear (2022)" << endl
164-
<< "Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals." << endl
181+
<< "Assessing Confidence in Root Placement on Phylogenies:" << endl
182+
<< "An Empirical Study Using Nonreversible Models for Mammals." << endl
165183
<< "Systematic Biology, 71:959–972." << endl
166184
<< "https://doi.org/10.1093/sysbio/syab067" << endl << endl;
167185
}
168186

169187
if (params.model_name.find("+H") != string::npos) {
170-
out << "To cite the GHOST \"+H\" please use: " << endl << endl
171-
<< "Stephen M Crotty, Bui Quang Minh, Nigel G Bean, Barbara R Holland, Jonathan Tuke, Lars S Jermiin, Arndt Von Haeseler (2020)" << endl
188+
out << "Since you used the GHOST \"+H\" model please also cite: " << endl << endl
189+
<< "Stephen M Crotty, Bui Quang Minh, Nigel G Bean, Barbara R Holland," << endl
190+
<< "Jonathan Tuke, Lars S Jermiin, Arndt Von Haeseler (2020)" << endl
172191
<< "GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments." << endl
173192
<< "Systematic Biology, 69:249-264." << endl
174193
<< "https://doi.org/10.1093/sysbio/syz051" << endl << endl;
175194
}
176195

177196
if (params.symtest != SYMTEST_NONE) {
178-
out << "To cite tests of symmetry please use: " << endl << endl
197+
out << "Since you used tests of symmetry please also cite: " << endl << endl
179198
<< "Suha Naser-Khdour, Bui Quang Minh, Wenqi Zhang, Eric A Stone, Robert Lanfear (2019)" << endl
180199
<< "The Prevalence and Impact of Model Violations in Phylogenetic Analysis." << endl
181200
<< "Genome Biology and Evolution, 11:3341-3352." << endl
@@ -191,7 +210,7 @@ void reportReferences(Params &params, ofstream &out) {
191210
// }
192211

193212
if (params.model_name.substr(0,4) == "TEST" || params.model_name.substr(0, 2) == "MF" || params.model_name.empty()) {
194-
out << "To cite ModelFinder please use: " << endl << endl
213+
out << "Since you used ModelFinder please also cite: " << endl << endl
195214
<< "Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler," << endl
196215
<< "and Lars S Jermiin (2017) ModelFinder: Fast model selection for" << endl
197216
<< "accurate phylogenetic estimates. Nature Methods, 14:587–589." << endl
@@ -200,7 +219,7 @@ void reportReferences(Params &params, ofstream &out) {
200219
modelfinder_only = true;
201220
}
202221
if (posPOMO(params.model_name) != string::npos) {
203-
out << "For polymorphism-aware models please cite:" << endl << endl
222+
out << "Since you used polymorphism-aware models please also cite:" << endl << endl
204223
<< "Dominik Schrempf, Bui Quang Minh, Arndt von Haeseler, Carolin Kosiol (2019)" << endl
205224
<< "Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity" << endl
206225
<< "Molecular Biology and Evolution, 36:1294–1301." << endl

‎utils/tools.cpp‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5538,11 +5538,11 @@ void parseArg(int argc, char *argv[], Params &params) {
55385538
params.dating_method = argv[cnt];
55395539
if (params.dating_method != "LSD"){
55405540
if (params.dating_method != "mcmctree"){
5541-
throw "Currently only LSD (least-square dating) method or MCMCTree method is supported";
5542-
continue;
5541+
throw "Use --dating LSD or --dating mcmctree";
55435542
}
55445543

55455544
}
5545+
continue;
55465546
}
55475547

55485548
if (strcmp(argv[cnt], "--date") == 0) {

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