Merge branch 'master' of https://github.com/iqtree/iqtree2

README.md

@@ -37,46 +37,99 @@ The strength of IQ-TREE is the availability of a wide variety of phylogenetic mo
 IQ-TREE web service
 -------------------
 
-For a quick start you can also try the IQ-TREE web server, which performs online computation using a dedicated computing cluster. It is very easy to use with as few as just 3 clicks! Try it out at
-
-<http://iqtree.cibiv.univie.ac.at>
+For a quick start you can also try the IQ-TREE web server, which performs 
+online computation using a dedicated computing cluster. It is very easy to use 
+with as few as just 3 clicks! Try it out at:
 
+* Vienna Bioinformatics Cluster: <http://iqtree.cibiv.univie.ac.at>
+* CIPRES Gateway: <https://www.phylo.org>
+* Los Alamos Laboratories: <https://www.hiv.lanl.gov/content/sequence/IQTREE/iqtree.html>
 
 User support
 ------------
 
-Please refer to the [user documentation](http://www.iqtree.org/doc/) and [frequently asked questions](http://www.iqtree.org/doc/Frequently-Asked-Questions). If you have further questions, feedback, feature requests, and bug reports, please sign up the following Google group (if not done yet) and post a topic to the 
-
-<https://groups.google.com/d/forum/iqtree>
-
-_The average response time is one working day._
+Please refer to the [user documentation](http://www.iqtree.org/doc/) and 
+[frequently asked questions](http://www.iqtree.org/doc/Frequently-Asked-Questions). 
+If you have further questions and feedback, please create a topic at 
+[Github discussions](https://github.com/iqtree/iqtree2/discussions).
+For feature requests bug reports please post a topic at
+[Github issues](https://github.com/iqtree/iqtree2/issues).
 
 Citations
 ---------
 
-When using ModelFinder please cite:
+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>
 
-* 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 estimating amino-acid Q matrix please cite:
+
+* 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:
 
-* D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, and L.S. Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation. *Mol. Biol. Evol.*, in press. <https://doi.org/10.1093/molbev/msx281>
+* D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, and 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 (in press) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. *Syst. Biol.* <https://doi.org/10.1093/sysbio/syx068>
+* 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 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>
+* 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 polymorphism-aware models please cite:
 
-* D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, C. Kosiol (2016) 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>
+* D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, C. Kosiol (2016) 
+  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
 
@@ -85,7 +138,13 @@ Some parts of the code were taken from the following packages/libraries: [Phylog
 [SPRNG library](http://www.sprng.org), [Zlib library](http://www.zlib.net), [gzstream library](http://www.cs.unc.edu/Research/compgeom/gzstream/), [vectorclass library](http://www.agner.org/optimize/), [GNU scientific library](https://www.gnu.org/software/gsl/).
 
 
-IQ-TREE was partially funded by the [Austrian Science Fund - FWF](http://www.fwf.ac.at/) (grant no. I 760-B17 from 2012-2015 and and I 2508-B29 from 2016-2019) and the [University of Vienna](https://www.univie.ac.at/) (Initiativkolleg I059-N).
+IQ-TREE was funded by the [Austrian Science Fund - FWF](http://www.fwf.ac.at/) 
+(grant no. I 760-B17 from 2012-2015 and and I 2508-B29 from 2016-2019),
+the [University of Vienna](https://www.univie.ac.at/) (Initiativkolleg I059-N),
+the [Australian National University](https://www.anu.edu.au),
+[Chan-Zuckerberg Initiative](https://chanzuckerberg.com) (open source software for science grants),
+[Simons Foundation](https://www.simonsfoundation.org), [Moore Foundation](https://www.moore.org),
+and [Australian Research Council](https://www.arc.gov.au).
 
 
 [Anisimova et al., 2011]: http://dx.doi.org/10.1093/sysbio/syr041