update citations

README.md

@@ -58,23 +58,41 @@ For feature requests bug reports please post a topic at
 Citations
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+When using tree mixture models (MAST) please cite:
+
+* T.K.F. Wong, C. Cherryh, A.G. Rodrigo, M.W. Hahn, B.Q. Minh, R. Lanfear (2024)
+  MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.
+  _Syst. Biol._, in press. <https://doi.org/10.1093/sysbio/syae008>
+
+When computing concordance factors please cite:
+
+* Y.K. Mo, R. Lanfear, M.W. Hahn, B.Q. Minh (2023)
+  Updated site concordance factors minimize effects of homoplasy and taxon sampling.
+  _Bioinformatics_, 39:btac741. <https://doi.org/10.1093/bioinformatics/btac741>
+
 When using AliSim to simulate alignments please cite:
 
 * N. Ly-Trong, S. Naser-Khdour, R. Lanfear, B.Q. Minh (2022)
   AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era.
   *Mol. Biol. Evol.*, 39:msac092. <https://doi.org/10.1093/molbev/msac092>
 
-When using ModelFinder please cite:
+When estimating amino-acid Q matrix 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>
+* B.Q. Minh, C. Cao Dang, L.S. Vinh, R. Lanfear (2021)
+  QMaker: Fast and accurate method to estimate empirical models of protein evolution.
+  _Syst. Biol._, 70:1046–1060. <https://doi.org/10.1093/sysbio/syab010>
+
+When using the heterotachy GHOST model "+H" 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 performing tree reconstruction please cite:
 
-* L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and 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>
+* 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>
 
 For the ultrafast bootstrap (UFBoot) please cite:
 
@@ -89,6 +107,12 @@ When using posterior mean site frequency model (PMSF) please cite:
   accelerates accurate phylogenomic estimation. 
   *Syst. Biol.*, 67:216–235. <https://doi.org/10.1093/sysbio/syx068>
 
+When using 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) 
@@ -101,6 +125,12 @@ When using polymorphism-aware models please cite:
   Reversible polymorphism-aware phylogenetic models and their application to tree inference. 
   *J. Theor. Biol.*, 407:362-370. <https://doi.org/10.1016/j.jtbi.2016.07.042>
 
+When using IQ-TREE version 1 please cite:
+
+* L. 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. and Evol._, 32:268-274. <https://doi.org/10.1093/molbev/msu300>
+
 #### Credits and Acknowledgements
 
 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),