The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Open accessAbstract
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“The model implemented in BEAST2 allows transitions between conserved and accelerated rates in both directions.”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Bouckaert et al. 2014
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“As seen in figure 3, the accuracy of both methods increases as the ratio between accelerated and conserved rates increases”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Bouckaert et al. 2014
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
BEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 13,104
Self-citationTamura, K., & Nei, M. (1993) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040023 · Cited by 11,267
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss075 · Cited by 10,128
Self-citationDating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · cited 1×
“In particular it implements relaxed clocks [3], non-parametric coalescent analysis [4,5], multispecies coalescent inference [6], phylogeography [7,8] and others.”
MethodSelf-citationBayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
Drummond, A. J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi103 · Cited by 3,094
Self-citation(1986) · Cited by 2,570
Bayesian inference of species trees from multilocus data
Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Items 801–900 of 1,007
Noguerales, V., Cordero, P. J., & Ortego, J. (2018) · Molecular Ecology · doi:10.1111/mec.14504 · Cited by 50
Klockgether, J., Cramer, N., Fischer, S., Wiehlmann, L., & Tümmler, B. (2018) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2017-0356oc · Cited by 50
Zhang, Z., Zhao, P., & Cai, L. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01407 · Cited by 50
Madzia, D., & Cau, A. (2020) · PeerJ · doi:10.7717/peerj.8941 · Cited by 52
Firneno, T. J., O’Neill, J. R., Portik, D. M., Emery, A. H., Townsend, J. H., & Fujita, M. K. (2020) · Molecular Ecology · doi:10.1111/mec.15496 · Cited by 50
Vargas, O. M., Goldston, B., Grossenbacher, D. L., & Kay, K. M. (2020) · Evolution · doi:10.1111/evo.14108 · Cited by 50
Chen, N., Ren, L., Du, L., Hou, J., Mullin, V. E., Wu, D., Zhao, X., Li, C., Huang, J.-H., Qi, X., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2011696117 · Cited by 50
Alter, S. E., Munshi‐South, J., & Stiassny, M. L. J. (2016) · Molecular Ecology · doi:10.1111/mec.13973 · Cited by 50
Jones, M. R., Mills, L. S., Jensen, J. D., & Good, J. M. (2020) · Evolution · doi:10.1111/evo.13976 · Cited by 49
Pirani, R. M., Peloso, P. L. V., do Prado, J. R., Polo, É. M., Knowles, L. L., Ron, S. R., Rodrigues, M. T., Sturaró, M. J., & Werneck, F. P. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106877 · Cited by 49
Guo, X., Mandáková, T. M., Trachtová, K., Özüdoğru, B., Liu, J., & Lysák, M. A. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa327 · Cited by 50
Barker, C. T., Hone, D. W. E., Naish, D., Cau, A., Lockwood, J. A. F., Foster, B., Clarkin, C., Schneider, P., & Gostling, N. J. (2021) · Scientific Reports · doi:10.1038/s41598-021-97870-8 · Cited by 49
Why do some bird species incorporate more anthropogenic materials into their nests than others?
Jagiello, Z. A., Reynolds, S. J., Nagy, J., Mainwaring, M. C., & Ibáñez‐Álamo, J. D. (2023) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2022.0156 · Cited by 63
Jurado‐Rivera, J. A., Pons, J., Álvarez, F., Botello, A., Humphreys, W. F., Page, T. J., Iliffe, T. M., Willassen, E., Meland, K., Juan, C., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-03107-y · Cited by 49
From America to Eurasia: a multigenomes history of the genus Abies
Семерикова, С. А., Khrunyk, Y. Y., Lascoux, M., & Semerikov, V. L. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.03.009 · Cited by 49
Hórreo, J. L., Peláez, M. L., Suárez, T., Breedveld, M. C., Heulin, B., Surget‐Groba, Y., Oksanen, T. A., & Fitze, P. S. (2018) · Journal of Biogeography · doi:10.1111/jbi.13349 · Cited by 49
Aghová, T., Palupčíková, K., Šumbera, R., Frynta, D., Lavrenchenko, L. A., Meheretu, Y., Sádlová, J., Votýpka, J., Mbau, J. S., Modrý, D., et al. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1380-9 · Cited by 49
Lee, H. O., Joh, H. J., Kim, K., Lee, S., Kim, N., Park, J. Y., Park, H.-S., Park, M.-S., Kim, S., Kwak, M., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20092196 · Cited by 49
Semo, A., Gayà‐Vidal, M., Fortes‐Lima, C., Alard, B., Oliveira, S., Almeida, J., Prista, A., Damasceno, A. A. M., Fehn, A., Schlebusch, C. M., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz224 · Cited by 49
Sholihah, A., Delrieu‐Trottin, E., Sukmono, T., Dahruddin, H., Risdawati, R., Elvyra, R., Wibowo, A., Kustiati, K., Busson, F., Sauri, S., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-59544-9 · Cited by 53
Goudet, M. M. M., Orr, D. J., Melkonian, M., Müller, K. H., Meyer, M. T., Carmo‐Silva, E., & Griffiths, H. (2020) · New Phytologist · doi:10.1111/nph.16577 · Cited by 50
A modern scleractinian coral with a two-component calcite–aragonite skeleton
Stolarski, J., Coronado, I., Murphy, J. G., Kitahara, M. V., Janiszewska, K., Mazur, M., Gothmann, A. M., Bouvier, A., Marin‐Carbonne, J., Taylor, M. L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013316117 · Cited by 49
Nge, F. J., Biffin, E., Thiele, K. R., & Waycott, M. (2021) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2020.616741 · Cited by 49
Solving the Coral Species Delimitation Conundrum
Ramírez‐Portilla, C., Baird, A. H., Cowman, P. F., Quattrini, A. M., Harii, S., Sinniger, F., & Flot, J. (2021) · Systematic Biology · doi:10.1093/sysbio/syab077 · Cited by 49
The role of prisons in disseminating tuberculosis in Brazil: A genomic epidemiology study
Walter, K. S., dos Santos, P. C. P., Gonçalves, T. O., da Silva, B. O., Santos, A. D. S., Leite, A. D. C., da Silva, A. M., Moreira, F. M. F., de Oliveira, R. D., Lemos, E. F., et al. (2022) · The Lancet Regional Health - Americas · doi:10.1016/j.lana.2022.100186 · Cited by 49
The genetics of morphological and behavioural island traits in deer mice
Baier, F., & Hoekstra, H. E. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.1697 · Cited by 48
A transmissible cancer shifts from emergence to endemism in Tasmanian devils
Patton, A. H., Lawrance, M. F., Margres, M. J., Kozakiewicz, C. P., Hamede, R., Ruiz‐Aravena, M., Hamilton, D. G., Comte, S., Ricci, L. E., Taylor, R. L., et al. (2020) · Science · doi:10.1126/science.abb9772 · Cited by 48
Tempo and drivers of plant diversification in the European mountain system
Smyčka, J., Roquet, C., Boleda, M., Alberti, A., Boyer, F., Douzet, R., Perrier, C., Rome, M., Valay, J.-G., Denœud, F., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30394-5 · Cited by 48
Jung, T., Milenković, I. L., Balcì, Y., Janoušek, J., Kudláek, T., Nagy, Z. Á., Baharuddin, B., Bakonyi, J., Broders, K. D., Cacciola, S. O., et al. (2024) · Studies in Mycology · doi:10.3114/sim.2024.107.04 · Cited by 48
Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus
de Melo, V. W., Ali, H. S., Freise, J., Kühnert, D., Essbauer, S. S., Mertens, M., Wanka, K. M., Drewes, S., Ulrich, R. G., & Heckel, G. (2015) · Evolutionary Applications · doi:10.1111/eva.12263 · Cited by 48
Self-citationEvaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
Duchêne, D. A., Duchêne, S., Holmes, E. C., & Ho, S. Y. W. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv154 · Cited by 49
Haemosporidian Parasites of Antelopes and Other Vertebrates from Gabon, Central Africa
Boundenga, L., Makanga, B. K., Ollomo, B., Gilabert, A., Rougeron, V., Mvé-Ondo, B., Arnathau, C., Durand, P., Moukodoum, N. D., Okouga, A.-P., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0148958 · Cited by 48
Glaser, L., Carstensen, M., Shaw, S. L., Robbe‐Austerman, S., Wünschmann, A., Grear, D. A., Stuber, T. P., & Thomsen, B. V. (2016) · PLoS ONE · doi:10.1371/journal.pone.0145735 · Cited by 48
Physalis and physaloids: A recent and complex evolutionary history
Zamora‐Tavares, P., Martínez, M., Magallón, S., Guzmán‐Dávalos, L., & Vargas‐Ponce, O. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.03.032 · Cited by 49
Co-circulation of two Usutu virus strains in Northern Italy between 2009 and 2014
Calzolari, M., Chiapponi, C., Bonilauri, P., Lelli, D., Baioni, L., Barbieri, I., Lavazza, A., Pongolini, S., Dottori, M., & Moreno, A. M. (2017) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2017.03.022 · Cited by 48
Phylogenetic Inference Using RevBayes
Höhna, S., Landis, M. J., & Heath, T. A. (2017) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.22 · Cited by 48
Hauenschild, F., Favre, A., Schnitzler, J., Michalak, I., Freiberg, M., & Muellner-Riehl, A. N. (2017) · Acta Botanica Yunnanica · doi:10.1016/j.pld.2017.05.010 · Cited by 48
Bell, R. C., Parra, J. L., Badjedjea, G., Barej, M. F., Blackburn, D. C., Burger, M., Channing, A., Dehling, J. M., Greenbaum, E., Gvoždík, V., et al. (2017) · Molecular Ecology · doi:10.1111/mec.14260 · Cited by 49
Conserved roles of Osiris genes in insect development, polymorphism and protection
Smith, C. R., Morandin, C., Noureddine, M., & Pant, S. (2018) · Journal of Evolutionary Biology · doi:10.1111/jeb.13238 · Cited by 49
Cortés, A. J., Gutiérrez, L. N. G., Garcia, J. B. V., & Madriñán, S. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.01700 · Cited by 50
Yang, Z., Wang, G., Ma, Q., Ma, W., Liang, L., & Zhao, T. (2019) · PeerJ · doi:10.7717/peerj.6320 · Cited by 48
Ochoa-Sánchez, L. E., & Vinuesa, P. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01548 · Cited by 48
Uncovering the evolutionary origin of blue anthocyanins in cereal grains
Jia, Y., Selva, C., Zhang, Y., Li, B., McFawn, L., Broughton, S., Zhang, X., Westcott, S., Wang, P., Tan, C., et al. (2019) · The Plant Journal · doi:10.1111/tpj.14557 · Cited by 48
Subbotin, S. A., Franco, J., Knoetze, R., Roubtsova, T. V., Bostock, R. M., & Vera, I. C. D. P. (2019) · Nematology · doi:10.1163/15685411-00003305 · Cited by 48
Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain
van Dorp, L., Gelabert, P., Rieux, A., de Manuel, M., de-Dios, T., Gopalakrishnan, S., Carøe, C., Sandoval‐Velasco, M., Fregel, R., Olalde, Í., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz264 · Cited by 53
Silva, C. S., Cordeiro, E. M. G., de Paiva, J. B., Dourado, P. M., Carvalho, R. A., Head, G., Martinelli, S., & Corrêa, A. S. (2020) · Evolutionary Applications · doi:10.1111/eva.12966 · Cited by 48
Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies
Didelot, X., Siveroni, I. A., & Volz, E. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa193 · Cited by 48
Wang, T., Zhang, Y., Yang, Z., Liu, Z., & Du, Y. (2020) · BMC Evolutionary Biology · doi:10.1186/s12862-020-01718-0 · Cited by 50
Larouche, O., Gartner, S. M., Westneat, M. W., & Evans, K. M. (2022) · Systematic Biology · doi:10.1093/sysbio/syac061 · Cited by 48
Nardo, A. D., Luca Ferretti, A., Wadsworth, J., Mioulet, V., Gelman, B., Karniely, S., Scherbakov, A. V., Ziay, G. M., Özyörük, F., Parlak, Ü., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab172 · Cited by 47
Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae)
Xiao, T., & Ge, X. (2022) · BMC Genomics · doi:10.1186/s12864-022-08855-4 · Cited by 48
Andersen, M. J., Hosner, P. A., Filardi, C. E., & Moyle, R. G. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.11.010 · Cited by 47
Stervander, M., Illera, J. C., Kvist, L., Barbosa, P., Keehnen, N. L. P., Pruisscher, P., Bensch, S., & Hansson, B. (2015) · Molecular Ecology · doi:10.1111/mec.13145 · Cited by 47
Ward, P. S., & Fisher, B. L. (2016) · Systematic Entomology · doi:10.1111/syen.12186 · Cited by 47
Psonis, N., Antoniou, A., Kukushkin, O. V., Jablonski, D., Petrov, B. P., Crnobrnja‐Isailović, J., Sotiropoulos, K., Gherghel, I., Lymberakis, P., & Poulakakis, N. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.09.007 · Cited by 47
Liu, P., Wen, J., Duan, L., Arslan, E., Ertuğrul, K., & Chang, Z. (2017) · PLoS ONE · doi:10.1371/journal.pone.0170596 · Cited by 47
Araújo, R., Buckley, D., Nagel, K., García-Jiménez, R., & Machordom, A. (2017) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlx039 · Cited by 49
Yermanos, A., Greiff, V., Kräutler, N. J., Menzel, U., Dounas, A., Miho, E., Oxenius, A., Stadler, T., & Reddy, S. T. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx533 · Cited by 47
Eilertsen, M. H., Georgieva, M. N., Kongsrud, J. A., Linse, K., Wiklund, H., Glover, A. G., & Rapp, H. T. (2018) · Scientific Reports · doi:10.1038/s41598-018-23076-0 · Cited by 47
Buzatti, R. S. D. O., Pfeilsticker, T. R., de Magalhães, R. F., Bueno, M. L., de Lemos-Filho, J. P., & Lovato, M. B. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00981 · Cited by 47
Charles, K. L., Bell, R. C., Blackburn, D. C., Burger, M., Fujita, M. K., Gvoždík, V., Jongsma, G. F. M., Kouete, M. T., Leaché, A. D., & Portik, D. M. (2018) · Journal of Biogeography · doi:10.1111/jbi.13365 · Cited by 47
Sequence comparison in computational historical linguistics
List, J., Walworth, M., Greenhill, S. J., Tresoldi, T., & Forkel, R. (2018) · Journal of Language Evolution · doi:10.1093/jole/lzy006 · Cited by 47
Bittencourt, P., Campos, Z., Muniz, F., Marioni, B., Souza, B. C., Silveira, R. D., de Thoisy, B., Hrbek, T., & Farias, I. P. (2019) · PeerJ · doi:10.7717/peerj.6580 · Cited by 47
Raman, G., Park, S., Lee, E. M., & Park, S. (2019) · Scientific Reports · doi:10.1038/s41598-019-41377-w · Cited by 47
Modifications during Early Plant Development Promote the Evolution of Nature’s Most Complex Woods
Onyenedum, J. G., Pace, M. R., Acevedo‐Rodríguez, P., Specht, C. D., & Rothfels, C. J. (2019) · Current Biology · doi:10.1016/j.cub.2019.11.003 · Cited by 47
Myers, E. A., McKelvy, A. D., & Burbrink, F. T. (2020) · Molecular Ecology · doi:10.1111/mec.15358 · Cited by 47
Limmon, G. V., Delrieu‐Trottin, E., Patikawa, J., Rijoly, F., Dahruddin, H., Busson, F., Steinke, D., & Hubert, N. (2020) · Ecology and Evolution · doi:10.1002/ece3.6128 · Cited by 47
Jara, M., Rasmussen, D. A., Corzo, C. A., & Machado, G. (2020) · Transboundary and Emerging Diseases · doi:10.1111/tbed.13728 · Cited by 47
Diversity patterns and evolutionary history of Arabian squamates
Šmı́d, J., Sindaco, R., Shobrak, M., Busais, S., Tamar, K., Aghová, T., Simó‐Riudalbas, M., Tarroso, P., Géniez, P., Crochet, P., et al. (2021) · Journal of Biogeography · doi:10.1111/jbi.14070 · Cited by 48
Salis, A. T., Bray, S. C. E., Lee, M. S. Y., Heiniger, H., Barnett, R., Burns, J. A., Doronichev, V. B., Fedje, D. W., Golovanova, L. V., Harington, C. R., et al. (2021) · Molecular Ecology · doi:10.1111/mec.16267 · Cited by 47
Zhou, T., Zhu, H., Wang, J., Xu, Y., Xu, F., & Wang, X. (2020) · Plant Cell Reports · doi:10.1007/s00299-020-02532-0 · Cited by 46
Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi
Scherz, M. D., Masonick, P., Meyer, A., & Hulsey, C. D. (2022) · Systematic Biology · doi:10.1093/sysbio/syac006 · Cited by 47
Continued evolution of the Eurasian avian-like H1N1 swine influenza viruses in China
Meng, F., Chen, Y., Song, Z., Zhong, Q., Zhang, Y., Qiao, C., Yan, C., Kong, H., Liu, L., Li, C., et al. (2022) · Science China Life Sciences · doi:10.1007/s11427-022-2208-0 · Cited by 46
A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)
Quek, Z. B. R., Jain, S. S., Richards, Z. T., Arrigoni, R., Benzoni, F., Hoeksema, B. W., Carvajal, J. I., Wilson, N. G., Baird, A. H., Kitahara, M. V., et al. (2023) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2023.107867 · Cited by 46
Mark, K., Saag, L., Leavitt, S. D., Will‐Wolf, S., Nelsen, M. P., Tõrra, T., Saag, A., Randlane, T., & Lumbsch, H. T. (2016) · Organisms Diversity & Evolution · doi:10.1007/s13127-016-0273-7 · Cited by 46
Bayesian phylogenetic estimation of fossil ages
Drummond, A. J., & Stadler, T. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0129 · Cited by 46
Self-citationFull circumpolar migration ensures evolutionary unity in the Emperor penguin
Cristofari, R., Bertorelle, G., Ancel, A., Benazzo, A., Maho, Y. L., Ponganis, P. J., Stenseth, N. C., Trathan, P. N., Whittington, J. D., Zanetti, E., et al. (2016) · Nature Communications · doi:10.1038/ncomms11842 · Cited by 46
Willet be one species or two? A genomic view of the evolutionary history of Tringa semipalmata
Oswald, J. A., Harvey, M. G., Remsen, R. C., Foxworth, D. U., Cardiff, S. W., Dittmann, D. L., Megna, L. C., Carling, M. D., & Brumfield, R. T. (2016) · The Auk · doi:10.1642/auk-15-232.1 · Cited by 46
Izumitani, H. F., Kusaka, Y., Koshikawa, S., Toda, M. J., & Katoh, T. (2016) · PLoS ONE · doi:10.1371/journal.pone.0160051 · Cited by 46
Inferring Ancestral Recombination Graphs from Bacterial Genomic Data
Vaughan, T. G., Welch, D., Drummond, A. J., Biggs, P. J., George, T., & French, N. P. (2016) · Genetics · doi:10.1534/genetics.116.193425 · Cited by 50
Self-citationHistorical Biogeography of endemic seed plant genera in the Caribbean: Did GAAR landia play a role?
Nieto‐Blázquez, M. E., Antonelli, A., & Roncal, J. (2017) · Ecology and Evolution · doi:10.1002/ece3.3521 · Cited by 46
Renner, S. S., Sousa, A., & Chomicki, G. (2017) · Taxon · doi:10.12705/666.7 · Cited by 46
Schield, D. R., Adams, R. H. J., Card, D. C., Corbin, A. B., Ježková, T., Hales, N. R., Meik, J. M., Perry, B. W., Spencer, C., Smith, L. L., et al. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.06.013 · Cited by 46
Chan, K. O., Grismer, L. L., & Brown, R. M. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.07.005 · Cited by 46
Zinner, D. P., Atickem, A., Beehner, J. C., Bekele, A., Bergman, T. J., Burke, R. J., Dolotovskaya, S., Fashing, P. J., Gippoliti, S., Knauf, S., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0202303 · Cited by 46
Piewbang, C., Radtanakatikanon, A., Puenpa, J., Poovorawan, Y., & Techangamsuwan, S. (2019) · Scientific Reports · doi:10.1038/s41598-019-39413-w · Cited by 46
Munro, J. T., Medina, I., Walker, K. L., Moussalli, A., Kearney, M., Dyer, A. G., García, J. E., Rankin, K. J., & Stuart-Fox, D. M. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.0234 · Cited by 46
Schäffer, S., Kerschbaumer, M., & Koblmüller, S. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.03.008 · Cited by 46
Hirano, T., Saito, T., Tsunamoto, Y., Koseki, J., Ye, B., Do, V. T., Miura, O., Suyama, Y., & Chiba, S. (2019) · Scientific Reports · doi:10.1038/s41598-019-42682-0 · Cited by 46
Evans, K. M., Vidal‐García, M., Tagliacollo., V. A., Taylor, S. J., & Fenolio, D. B. (2019) · Integrative and Comparative Biology · doi:10.1093/icb/icz026 · Cited by 46
Jambura, P. L., Kindlimann, R., López‐Romero, F. A., Marramà, G., Pfaff, C., Stumpf, S., Türtscher, J., Underwood, C. J., Ward, D. J., & Kriwet, J. (2019) · Scientific Reports · doi:10.1038/s41598-019-46081-3 · Cited by 46
Reyes‐Velasco, J., Adams, R. H. J., Boissinot, S., Parkinson, C. L., Campbell, J. A., Castoe, T. A., & Smith, E. N. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106770 · Cited by 46
Wang, W., Xiang, X., Xiang, K., Ortiz, R. D. C., Jabbour, F., & Chen, Z. (2020) · Cladistics · doi:10.1111/cla.12414 · Cited by 46
Jamrozy, D. M., Bijlsma, M. W., de Goffau, M. C., van de Beek, D., Kuijpers, T. W., Parkhill, J., ENDE, A. V. D., & Bentley, S. D. (2020) · Scientific Reports · doi:10.1038/s41598-020-66214-3 · Cited by 48
Hameed, M., Wahaab, A., Shan, T., Wang, X., Khan, S., Di, D., Liu, X., Zhang, J., Anwar, M. N., Nawaz, M., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.591478 · Cited by 46
Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards
Esquerré, D., Keogh, J. S., Demangel, D., Morando, M. M., Ávila, L. J., Sites, J. W., Ferri‐Yáñez, F., & Leaché, A. D. (2021) · Systematic Biology · doi:10.1093/sysbio/syab058 · Cited by 49
An empirical guide for producing a dated phylogeny with treePL in a maximum likelihood frameworkPreprint
Maurin, K. J. L. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2008.07054 · Cited by 46
Cerca, J., Meyer, C., Purschke, G., & Struck, T. H. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106663 · Cited by 45
Li, H., Wu, Y., Feng, D., Jiang, Q., Li, S., Rong, J., Zhong, L., Methner, U., Baxter, L. A., Ott, S., et al. (2024) · Nature Food · doi:10.1038/s43016-024-00968-1 · Cited by 45
Aduse‐Poku, K., Brattström, O., Kodandaramaiah, U., Lees, D. C., Brakefield, P. M., & Wahlberg, N. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0449-3 · Cited by 45
Metadata
- Authors
- Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J.
- Affiliations
- University of Auckland (NZ)
- University of California, Los Angeles (US)
- University of Edinburgh (GB)
- Corresponding author
- Bouckaert, Remco
- Drummond, Alexei J.
- ORCID
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-04-10
- Volume
- 10
- Issue
- 4
- Pages
- e1003537
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC3985171
- OpenAlex
- W2026062398
- Cited by
- 6,527
- References
- 31
- Citations by year
- 2026: 364 · 2025: 464 · 2024: 509 · 2023: 492 · 2022: 588 · 2021: 745 · 2020: 801 · 2019: 784 · 2018: 724 · 2017: 484 · 2016: 302 · 2015: 213 · 2014: 44
- FWCI
- 131.24
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository for Publications and Research Data (ETH Zurich) (publishedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- ePrints Soton (University of Southampton) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- ResearchSpace (University of Auckland) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Funders
- National Science Foundation (1264153, 0856099)
- National Evolutionary Synthesis Center
- Wellcome Trust (095831)
- Royal Society
- Royal Society Te Apārangi
- National Institutes of Health
- National Human Genome Research Institute (R01HG006139)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- BEAST2, Bayesian phylogenetics, Markov chain Monte Carlo, package management, extensibility, phylodynamics, model averaging, substitution models, XML file format, open source software
- MeSH terms
- Bayes Theorem, Biological Evolution, Programming Languages, Software
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
