ModelFinder: fast model selection for accurate phylogenetic estimates
Open accessAbstract
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
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The K2P + R2 model was selected by ModelFinder before computing the tree.
“The K2P + R2 model was selected by ModelFinder before computing the tree [64].”
From Emergent and Neglected Equine Filariosis in Egypt: Species Diversity and Host Immune Response (2022) · cites this paper as [64]
Best-fit partitions and substitution models were inferred with ModelFinder as implemented in IQ-TREE 1.6.12 with 20% relaxed clustering.
“Best-fit partitions and substitution models were inferred with ModelFinder 12 , as implemented in IQ-TREE 1.6.12 2 , with 20% relaxed clustering”
From Available data do not rule out Ctenophora as the sister group to all other Metazoa (2023) · cites this paper as [12]
In clinical studies of BNT162b2, high levels of protection against infection and severe disease were observed after the second dose.
“In clinical studies of the Pfizer-BioNTech BNT162b2 vaccine, high levels of protection against infection and severe disease were observed after the second dose10.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [10]
Licensed SARS-CoV-2 vaccines target the spike protein and have protection rates ranging from 62 to 95%.
“SARS-CoV-2 vaccines have recently been licensed that target the spike (S) protein, either using mRNA or adenovirus vector technology with protection rates ranging from 62 to 95%9–11.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [10]
The high performance of IQ-TREE results from the efficient integration of novel phylogenetic methods that improve the three key steps in phylogenetic analysis: fast model selection via ModelFinder, an effective tree search algorithm, and a novel ultrafast bootstrap approximation.
“The high performance of IQ-TREE results from the efficient integration of novel phylogenetic methods that improve the three key steps in phylogenetic analysis: fast model selection via ModelFinder (Kalyaanamoorthy et al. 2017), an effective tree search algorithm (Nguyen et al. 2015), and a novel ultrafast bootstrap approximation (Minh et al. 2013; Hoang et al. 2018).”
From IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2020) · cites this paper as Kalyaanamoorthy et al. 2017
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Cites
Maximum Likelihood from Incomplete Data Via the <i>EM</i> Algorithm
Dempster, A. P., Laird, N. M., & Rubin, D. B. (1977) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1977.tb01600.x · Cited by 50,444 · see citing works
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046 · see citing works
Self-citationMODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820 · see citing works
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376 · see citing works
jModelTest 2: more models, new heuristics and parallel computing
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012) · Nature Methods · doi:10.1038/nmeth.2109 · Cited by 16,828 · see citing works
Kass, R. E., & Raftery, A. E. (1995) · Journal of the American Statistical Association · doi:10.1080/01621459.1995.10476572 · Cited by 12,558 · see citing works
jModelTest: Phylogenetic Model Averaging
Posada, D. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn083 · Cited by 10,534 · see citing works
Practical Methods of Optimization
Fletcher, R. (2000) · Wiley eBooks · doi:10.1002/9781118723203 · Cited by 7,649 · see citing works
BEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527 · see citing works
Lanfear, R., Calcott, B., Ho, S. Y. W., & Guindon, S. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss020 · Cited by 5,732 · see citing works
An Improved General Amino Acid Replacement Matrix
Le, S. Q., & Gascuel, O. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn067 · Cited by 3,127 · see citing works
ProtTest: selection of best-fit models of protein evolution
Abascal, F., Zardoya, R., & Posada, D. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti263 · Cited by 3,063 · see citing works
Comparison of phylogenetic trees
Robinson, D. F., & Foulds, L. R. (1981) · Mathematical Biosciences · doi:10.1016/0025-5564(81)90043-2 · Cited by 2,990 · see citing works
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960 · see citing works
Algorithms for Minimization Without Derivatives
G., D., & Brent, R. P. (1974) · Mathematics of Computation · doi:10.2307/2005713 · Cited by 2,914 · see citing works
ProtTest 3: fast selection of best-fit models of protein evolution
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr088 · Cited by 2,677 · see citing works
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015) · Nature · doi:10.1038/nature15697 · Cited by 1,668 · see citing works
Keane, T., Creevey, C. J., Pentony, M. M., Naughton, T. J., & Mclnerney, J. O. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-29 · Cited by 1,070 · see citing works
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B. J., et al. (2009) · Nature · doi:10.1038/nature08656 · Cited by 998 · see citing works
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2016) · Nature · doi:10.1038/nature19417 · Cited by 928 · see citing works
ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2011) · Lecture notes in computer science · doi:10.1007/978-3-642-21878-1_22 · Cited by 811 · see citing works
Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary AnalysisPreprint
Eisen, J. A. (1998) · Genome Research · doi:10.1101/gr.8.3.163 · Cited by 628 · see citing works
Inferring ancient divergences requires genes with strong phylogenetic signals
Salichos, L., & Rokas, A. (2013) · Nature · doi:10.1038/nature12130 · Cited by 616 · see citing works
Ruhfel, B. R., Gitzendanner, M. A., Soltis, P. S., Soltis, P. S., & Burleigh, J. G. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-23 · Cited by 547 · see citing works
dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.0683 · Cited by 526 · see citing works
A space-time process model for the evolution of DNA sequences.
Yang, Z. (1995) · Genetics · doi:10.1093/genetics/139.2.993 · Cited by 432 · see citing works
INDELible: A Flexible Simulator of Biological Sequence Evolution
Fletcher, W., & Yang, Z. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp098 · Cited by 416 · see citing works
Posada, D. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl042 · Cited by 323 · see citing works
The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates
Soubrier, J., Steel, M., Lee, M. S. Y., Sarkissian, C. S. I. D., Guindon, S., Ho, S. Y. W., & Cooper, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss140 · Cited by 316 · see citing works
Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus
Andersen, K. G., Shapiro, B. J., Matranga, C. B., Sealfon, R. S. G., Lin, A. E., Moses, L., Folarin, O. A., Goba, A., Odia, I., Ehiane, P. E., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.020 · Cited by 302 · see citing works
Characterization of the type I interferon locus and identification of novel genes☆
Hardy, M. P., Owczarek, C. M., Jermiin, L. S., Ejdebäck, M., & Hertzog, P. J. (2004) · Genomics · doi:10.1016/j.ygeno.2004.03.003 · Cited by 238 · see citing works
Self-citationjmodeltest.org: selection of nucleotide substitution models on the cloud
Santorum, J. M., Darriba, D., Taboada, G. L., & Posada, D. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu032 · Cited by 96 · see citing works
Tay, W. T., Walsh, T., Downes, S. J., Anderson, C. J., Jermiin, L. S., Wong, T. K. F., Piper, M. C., Chang, E. S., Macedo, I. B., Czepak, C., et al. (2017) · Scientific Reports · doi:10.1038/srep45302 · Cited by 67 · see citing works
Self-citationJayaswal, V., Wong, T. K. F., Robinson, J., Poladian, L., & Jermiin, L. S. (2014) · Systematic Biology · doi:10.1093/sysbio/syu036 · Cited by 66 · see citing works
Self-citationA Molecular Framework for the Phylogeny of the Ant Subfamily Dolichoderinae
Chiotis, M., Jermiin, L. S., & Crozier, R. H. (2000) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.2000.0821 · Cited by 59 · see citing works
Self-citationHigh chromosome numbers in Mojavean and Sonoran desert Atriplex canescens (Chenopodiaceae)
Sanderson, S. C., & Stutz, H. C. (1994) · American Journal of Botany · doi:10.1002/j.1537-2197.1994.tb15593.x · Cited by 49 · see citing works
Whelan, S., Allen, J. E., Blackburne, B. P., & Talavera, D. (2014) · Systematic Biology · doi:10.1093/sysbio/syu062 · Cited by 47 · see citing works
Guindon, S. (2012) · Systematic Biology · doi:10.1093/sysbio/sys063 · Cited by 41 · see citing works
Flagged first, then by citations
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Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873 · see citing works
Self-citationHuerta‐Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunić, I., Rattei, T., Jensen, L. J., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1085 · Cited by 4,943 · see citing works
Zhang, D., Gao, F., Jakovlić, I., Jakovlić, I., Zou, H., Zhang, J., & Wang, G. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13096 · Cited by 4,122 · see citing works
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
Darriba, D., Posada, D., Kozlov, A. M., Stamatakis, A., Morel, B., & Flouri, T. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz189 · Cited by 2,128 · see citing works
Feiner, N., Motone, F., Meyer, A., & Kuraku, S. (2019) · Scientific Reports · doi:10.1038/s41598-019-40055-1 · Cited by 1,988 · see citing works
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., et al. (2021) · Nature · doi:10.1038/s41586-021-03291-y · Cited by 1,097 · see citing works
Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction
Koblan, L. W., Doman, J. L., Wilson, C., Levy, J. M., Tay, T., Newby, G. A., Maianti, J. P., Raguram, A., & Liu, D. R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4172 · Cited by 944 · see citing works
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R., Walls, A. C., Kemp S, S. A., Bassi, J., Pinto, D., Fregni, C. S., et al. (2021) · doi:10.1101/2021.01.19.21249840 · Cited by 729 · see citing works
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., Kemp, S. A., Bassi, J., Pinto, D., Silacci-Fregni, C., et al. (2021) · Nature · doi:10.1038/s41586-021-03412-7 · Cited by 728 · see citing works
Sensitivity and specificity of information criteria
(2019) · doi:10.1093/bib/bbz016 · Cited by 718 · see citing works
Self-citationAvanzato, V. A., Matson, M. J., Seifert, S. N., Pryce, R., Williamson, B. N., Anzick, S. L., Barbian, K., Judson, S. D., Fischer, E. R., Martens, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.049 · Cited by 703 · see citing works
Helmy, Y. A., Fawzy, M., Elaswad, A., Sobieh, A., Kenney, S. P., & Shehata, A. A. (2020) · Journal of Clinical Medicine · doi:10.3390/jcm9041225 · Cited by 687 · see citing works
Waite, D. W., Chuvochina, M. S., Pelikan, C., Parks, D. H., Yilmaz, P., Wagner, M., Loy, A., Naganuma, T., Nakai, R., Whitman, W. B., et al. (2020) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.004213 · Cited by 655 · see citing works
Improved metagenome binning and assembly using deep variational autoencoders
Nissen, J. N., Johansen, J., Allesøe, R. L., Sønderby, C. K., Armenteros, J. J. A., Grønbech, C. H., Jensen, L. J., Nielsen, H. B., Petersen, T. N., Winther, O., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00777-4 · Cited by 634 · see citing works
Damas, J., Hughes, G. M., Keough, K. C., Painter, C. A., Persky, N. S., Corbo, M., Hiller, M., Koepfli, K.-P., Pfenning, A. R., Zhao, H., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2010146117 · Cited by 633 · see citing works
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Edelman, N. B., Frandsen, P. B., Miyagi, M., Clavijo, B., Davey, J. W., Dikow, R. B., Accinelli, G. G., Belleghem, S. M. V., Patterson, N. J., Neafsey, D. E., et al. (2019) · Science · doi:10.1126/science.aaw2090 · Cited by 612 · see citing works
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Turner, D., Kropinski, A. M., & Adriaenssens, E. M. (2021) · Viruses · doi:10.3390/v13030506 · Cited by 585 · see citing works
A reference genome for pea provides insight into legume genome evolution
Kreplak, J., Madoui, M., Cápal, P., Novák, P., Labadie, K., Aubert, G., Bayer, P. E., Gali, K. K., Syme, R. A., Main, D., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0480-1 · Cited by 549 · see citing works
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
von Meijenfeldt, F. A. B., Arkhipova, K., Cambuy, D. D., Coutinho, F., & Dutilh, B. (2019) · Genome Biology · doi:10.1186/s13059-019-1817-x · Cited by 503 · see citing works
Massive haplotypes underlie ecotypic differentiation in sunflowers
Todesco, M., Owens, G. L., Bercovich, N., Légaré, J.-S., Soudi, S., Burge, D. O., Huang, K., Ostevik, K. L., Drummond, E. B. M., Imerovski, I., et al. (2020) · Nature · doi:10.1038/s41586-020-2467-6 · Cited by 513 · see citing works
Phylogenetic tree building in the genomic age
Kapli, P., Yang, Z., & Telford, M. J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0233-0 · Cited by 533 · see citing works
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Cheng, S., Xian, W., Fu, Y., Marin, B., Keller, J., Wu, T., Sun, W., Li, X., Xu, Y., Zhang, Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.019 · Cited by 529 · see citing works
Outline of Fungi and fungus-like taxa – 2021
Wijayawardene, N., Hyde, K., Dai, D., Sánchez‐García, M., Goto, B., Saxena, R., Erdoğdu, M., Selçuk, F., Rajeshkumar, K. C., Aptroot, A., et al. (2022) · Mycosphere · doi:10.5943/mycosphere/13/1/2 · Cited by 523 · see citing works
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale
Liew, F. E., Nogle, R., Abdalla, T., Rasor, B. J., Canter, C. E., Jensen, R. O., Wang, L., Strutz, J., Chirania, P., Tissera, S. L. D., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01195-w · Cited by 487 · see citing works
Alanjary, M. M., Steinke, K., & Ziemert, N. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz282 · Cited by 469 · see citing works
COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
Naveca, F. G., do Nascimento, V. A., de Souza, V. C., Corado, A. D. L. G., Nascimento, F., Silva, G., Costa, Á., Duarte, D., Pessoa, K., Mejía, M., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01378-7 · Cited by 474 · see citing works
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Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G., Crook, M. B., Billault‐Penneteau, B., Lauressergues, D., Keller, J., Imanishi, L., et al. (2018) · Science · doi:10.1126/science.aat1743 · Cited by 457 · see citing works
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics
Bel, M. V., Diels, T., Vancaester, E., Kreft, Ł., Botzki, A., de Peer, Y. V., Coppens, F., & Vandepoele, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1002 · Cited by 451 · see citing works
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Altae-Tran, H., Kannan, S., Demircioglu, F. E., Oshiro, R., Nety, S. P., McKay, L. J., Dlakić, M., Inskeep, W. P., Makarova, K. S., Macrae, R. K., et al. (2021) · Science · doi:10.1126/science.abj6856 · Cited by 407 · see citing works
Deep mitochondrial origin outside the sampled alphaproteobacteria
Martijn, J., Vosseberg, J., Guy, L., Offre, P., & Ettema, T. J. G. (2018) · Nature · doi:10.1038/s41586-018-0059-5 · Cited by 378 · see citing works
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
Meng, B., Kemp, S. A., Papa, G., Datir, R. P., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109292 · Cited by 397 · see citing works
Meredith, L. W., Hamilton, W. L., Warne, B., Houldcroft, C. J., Hosmillo, M. D. T., Jahun, A. S., Curran, M. D., Parmar, S., Caller, L., Caddy, S., et al. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30562-4 · Cited by 387 · see citing works
Fusarium: more than a node or a foot-shaped basal cell
Crous, P. W., Lombard, L., Sandoval‐Denis, M., Seifert, K. A., Schroers, H., Chaverri-Echandi, P., Gené, J., Guarro, J., Hirooka, Y., Bensch, K., et al. (2021) · Studies in Mycology · doi:10.1016/j.simyco.2021.100116 · Cited by 385 · see citing works
A genome-scale phylogeny of the kingdom Fungi
Li, Y., Steenwyk, J. L., Chang, Y., Wang, Y., James, T. Y., Stajich, J., Spatafora, J. W., Groenewald, M., Dunn, C. W., Hittinger, C. T., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.01.074 · Cited by 373 · see citing works
Pearce, S. L., Clarke, D. F., East, P. D., Elfékih, S., Gordon, K. H. J., Jermiin, L. S., McGaughran, A., Oakeshott, J. G., Papanikolaou, A., Perera, O. P., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0402-6 · Cited by 356 · see citing works
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Jebb, D., Huang, Z., Pippel, M., Hughes, G. M., Lavrichenko, K., Devanna, P., Winkler, S., Jermiin, L. S., Skirmuntt, E. C., Katzourakis, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2486-3 · Cited by 361 · see citing works
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Zhu, Q.-Y., Mai, U., Pfeiffer, W., Janssen, S., Asnicar, F., Sanders, J. G., Belda-Ferre, P., Al-Ghalith, G., Kopylova, E., McDonald, D., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13443-4 · Cited by 309 · see citing works
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Alves, R. E., Minh, B. Q., Urich, T., von Haeseler, A., & Schleper, C. (2018) · Nature Communications · doi:10.1038/s41467-018-03861-1 · Cited by 341 · see citing works
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Burbrink, F. T., Grazziotin, F. G., Pyron, R. A., Cundall, D., Donnellan, S. C., Irish, F. J., Keogh, J. S., Kraus, F., Murphy, R. W., Noonan, B. P., et al. (2019) · Systematic Biology · doi:10.1093/sysbio/syz062 · Cited by 321 · see citing works
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Tonkin‐Hill, G. Q., Lees, J. A., Bentley, S. D., Frost, S. D. W., & Corander, J. (2018) · Wellcome Open Research · doi:10.12688/wellcomeopenres.14694.1 · Cited by 311 · see citing works
Antarctica’s ecological isolation will be broken by storm-driven dispersal and warming
Fraser, C. I., Morrison, A. K., Hogg, A. M., Macaya, E. C., van Sebille, E., Ryan, P. G., Padovan, A., Jack, C., Valdivia, N., & Waters, J. M. (2018) · Nature Climate Change · doi:10.1038/s41558-018-0209-7 · Cited by 306 · see citing works
Multiple lineages of monkeypox virus detected in the United States, 2021–2022
Gigante, C. M., Korber, B., Seabolt, M. H., Wilkins, K., Davidson, W., Rao, A. K., Zhao, H., Smith, T. G., Hughes, C. M., Minhaj, F. S., et al. (2022) · Science · doi:10.1126/science.add4153 · Cited by 302 · see citing works
Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis
Lee, J. Y. H., Monk, I. R., da Silva, A. G., Seemann, T., Chua, K., Kearns, A., Hill, R., Woodford, N., Bartels, M. D., Strommenger, B., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0230-7 · Cited by 299 · see citing works
Schilling, S., Kennedy, A., Pan, S., Jermiin, L. S., & Melzer, R. (2019) · New Phytologist · doi:10.1111/nph.16122 · Cited by 298 · see citing works
Self-citationIn honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma
Cai, F. M., & Druzhinina, I. S. (2021) · Fungal Diversity · doi:10.1007/s13225-020-00464-4 · Cited by 297 · see citing works
Schmitz, L., Yan, Z., Schneijderberg, M., de Roij, M., Pijnenburg, R., Zheng, Q., Franken, C., Dechesne, A. C., Trindade, L. M., van Velzen, R., et al. (2022) · The ISME Journal · doi:10.1038/s41396-022-01238-3 · Cited by 297 · see citing works
Integrated phylogenomics and fossil data illuminate the evolution of beetles
Cai, C., Tihelka, E., Giacomelli, M., Lawrence, J. F., Ślipiński, A., Kundrata, R., Yamamoto, S., Thayer, M. K., Newton, A. F., Leschen, R. A. B., et al. (2022) · Royal Society Open Science · doi:10.1098/rsos.211771 · Cited by 289 · see citing works
Phylum Gemmatimonadota and Its Role in the Environment
Mujakić, I., Piwosz, K., & Koblížek, M. (2022) · Microorganisms · doi:10.3390/microorganisms10010151 · Cited by 275 · see citing works
Sun, E., Huang, L., Zhang, X., Zhang, J., Shen, D., Zhang, Z., Wang, Z., Huo, H., Wang, W., Huangfu, H., et al. (2021) · Emerging Microbes & Infections · doi:10.1080/22221751.2021.1999779 · Cited by 271 · see citing works
Morales‐Briones, D. F., Kadereit, G., Tefarikis, D. T., Moore, M. J., Smith, S. A., Brockington, S. F., Timoneda, A., Yim, W. C., Cushman, J. C., & Yang, Y. J. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa066 · Cited by 260 · see citing works
Structure of the bacterial ribosome at 2 Å resolution
Watson, Z. L., Ward, F. R., Méheust, R., Ad, O., Schepartz, A., Banfield, J. F., & Cate, J. H. (2020) · eLife · doi:10.7554/elife.60482 · Cited by 263 · see citing works
Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia
Gaiti, F., Chaligne, R., Gu, H., Brand, R. M., Kothen-Hill, S., Schulman, R. C., Grigorev, K., Risso, D., Kim, K.-T., Pastore, A., et al. (2019) · Nature · doi:10.1038/s41586-019-1198-z · Cited by 262 · see citing works
Madhaiyan, M., Wirth, J. S., & Saravanan, V. S. (2020) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.004498 · Cited by 261 · see citing works
An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages
Radhakrishnan, G. V., Keller, J., Rich, M., Vernié, T., Mbadinga, D. L. M., Vigneron, N., Cottret, L., Clemente, H., Libourel, C., Cheema, J., et al. (2020) · Nature Plants · doi:10.1038/s41477-020-0613-7 · Cited by 191 · see citing works
Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities
Jung, M., Sedlacek, C. J., Kits, K. D., Mueller, A. J., Rhee, S., Hink, L., Nicol, G. W., Bayer, B., Lehtovirta‐Morley, L. E., Wright, C., et al. (2021) · The ISME Journal · doi:10.1038/s41396-021-01064-z · Cited by 257 · see citing works
Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses
Moniruzzaman, M., Martínez-Gutiérrez, C. A., Weinheimer, A., & Aylward, F. O. (2020) · Nature Communications · doi:10.1038/s41467-020-15507-2 · Cited by 255 · see citing works
Population sequencing enhances understanding of tea plant evolution
Wang, X., Hu, F., Chang, Y., Ma, C.-L., Wang, L., Hao, X., Li, A., Cheng, H., Wang, L., Cui, P., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18228-8 · Cited by 261 · see citing works
Highly lethal genotype I and II recombinant African swine fever viruses detected in pigs
Zhao, D., Sun, E., Huang, L., Ding, L., Zhu, Y., Zhang, J., Shen, D., Zhang, X., Zhang, Z., Ren, T., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38868-w · Cited by 252 · see citing works
Santos, P. E. L., Palmer, M., Chávez‐Ramírez, B., Beukes, C. W., Steenkamp, E. T., Briscoe, L., Khan, N., Maluk, M., Lafos, M., Humm, E. A., et al. (2018) · Genes · doi:10.3390/genes9080389 · Cited by 246 · see citing works
Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
Petit, R. A., & Read, T. D. (2020) · mSystems · doi:10.1128/msystems.00190-20 · Cited by 245 · see citing works
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M. C., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K. A., Barr, J. J., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0494-6 · Cited by 247 · see citing works
Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
Zayed, A. A., Wainaina, J. M., Domínguez‐Huerta, G., Pelletier, É., Guo, J., Mohssen, M., Tian, F., Pratama, A. A., Bolduc, B., Zablocki, O., et al. (2022) · Science · doi:10.1126/science.abm5847 · Cited by 223 · see citing works
Widespread soil bacterium that oxidizes atmospheric methane
Tveit, A. T., Hestnes, A. G., Robinson, S. L., Schintlmeister, A., Dedysh, S. N., Jehmlich, N., von Bergen�, M., Herbold, C. W., Wagner, M., Richter, A. A., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817812116 · Cited by 228 · see citing works
Payne, L. J., Todeschini, T. C., Wu, Y., Perry, B. J., Ronson, C. W., Fineran, P. C., Nóbrega, F. L., & Jackson, S. A. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab883 · Cited by 233 · see citing works
A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes
Johnston, P. R., Quijada, L., Smith, C. A., Baral, H.-O., Hosoya, T., Baschien, C., Pärtel, K., Zhuang, W.-Y., Haelewaters, D., DuckChul, P., et al. (2019) · IMA Fungus · doi:10.1186/s43008-019-0002-x · Cited by 228 · see citing works
Evangelista, D. A., Wipfler, B., Béthoux, O., Donath, A., Fujita, M., Kohli, M. K., Legendre, F., Liu, S., Machida, R., Misof, B. Y., et al. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.2076 · Cited by 222 · see citing works
Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
Kemp, S. A., Meng, B., Ferriera, I. A., Datir, R., Harvey, W. T., Papa, G., Lytras, S., Collier, D. A., Mohamed, A., Gallo, G., et al. (2020) · doi:10.1101/2020.12.14.422555 · Cited by 252 · see citing works
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses
Irwin, N. A. T., Pittis, A. A., Richards, T. A., & Keeling, P. J. (2021) · Nature Microbiology · doi:10.1038/s41564-021-01026-3 · Cited by 224 · see citing works
Lipid exchanges drove the evolution of mutualism during plant terrestrialization
Rich, M., Vigneron, N., Libourel, C., Keller, J., Xue, L., Hajheidari, M., Radhakrishnan, G. V., Ru, A. L., Diop, S., Potente, G., et al. (2021) · Science · doi:10.1126/science.abg0929 · Cited by 152 · see citing works
Plant Mating Systems Often Vary Widely Among Populations
Whitehead, M. R., Lanfear, R., Mitchell, R. J., & Karron, J. D. (2018) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2018.00038 · Cited by 219 · see citing works
Wirth, J. S., & Whitman, W. B. (2018) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.002833 · Cited by 217 · see citing works
Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics
Young, A. D., & Gillung, J. P. (2019) · Systematic Entomology · doi:10.1111/syen.12406 · Cited by 215 · see citing works
Pinnell, L. J., & Turner, J. W. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01252 · Cited by 212 · see citing works
Geiser, D. M., Al‐Hatmi, A. M. S., Aoki, T., Arie, T., Balmas, V., Barnes, I., Bergstrom, G. C., Bhattacharyya, M. K., Blomquist, C. L., Bowden, R. L., et al. (2020) · Phytopathology · doi:10.1094/phyto-08-20-0330-le · Cited by 212 · see citing works
A global catalog of whole-genome diversity from 233 primate species
Kuderna, L. F. K., Gao, H. C., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T. M., Manu, S., Valenzuela, A., Bergman, J., Rousselle, M. M. C., et al. (2023) · Science · doi:10.1126/science.abn7829 · Cited by 206 · see citing works
Denise, R., Abby, S., & Rocha, E. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000390 · Cited by 188 · see citing works
GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments
Crotty, S., Minh, B. Q., Bean, N. G., Holland, B. R., Tuke, J., Jermiin, L. S., & von Haeseler, A. (2019) · Systematic Biology · doi:10.1093/sysbio/syz051 · Cited by 206 · see citing works
Self-citationEnhanced rare-earth separation with a metal-sensitive lanmodulin dimer
Mattocks, J. A., Jung, J. J., Lin, C., Dong, Z., Yennawar, N. H., Featherston, E. R., Kang-Yun, C. S., Hamilton, T. A., Park, D. M., Boal, A. K., et al. (2023) · Nature · doi:10.1038/s41586-023-05945-5 · Cited by 208 · see citing works
Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines
Jin, W., Gernandt, D. S., Wehenkel, C., Xia, X., Wei, X., & Wang, X. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2022302118 · Cited by 209 · see citing works
Insights into the Diversification and Evolution of R2R3-MYB Transcription Factors in Plants
Jiang, C., & Rao, G. (2020) · PLANT PHYSIOLOGY · doi:10.1104/pp.19.01082 · Cited by 202 · see citing works
Sharrar, A. M., Crits‐Christoph, A., Méheust, R., Diamond, S., Starr, E. P., & Banfield, J. F. (2020) · mBio · doi:10.1128/mbio.00416-20 · Cited by 203 · see citing works
A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants
Dearlove, B. L., Lewitus, É., Bai, H., Li, Y., Reeves, D. B., Joyce, M. G., Scott, P. T., Amare, M. F., Vasan, S., Michael, N. L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2008281117 · Cited by 199 · see citing works
Actin cytoskeleton and complex cell architecture in an Asgard archaeon
Rodrigues-Oliveira, T., Wollweber, F., Ponce-Toledo, R. I., Xu, J., Rittmann, S. K. ‐. R., Klingl, A., Pilhofer, M., & Schleper, C. (2022) · Nature · doi:10.1038/s41586-022-05550-y · Cited by 196 · see citing works
Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae
Bossert, S., Murray, E. A., Almeida, E. A. B., Brady, S. G., Blaimer, B. B., & Danforth, B. N. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.10.012 · Cited by 196 · see citing works
Wipfler, B., Letsch, H. O., Frandsen, P. B., Kapli, P., Mayer, C., Bartel, D., Buckley, T. R., Donath, A., Edgerly, J. S., Fujita, M., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817794116 · Cited by 198 · see citing works
Abdullah, A., Mehmood, F., Shahzadi, I., Waseem, S., Mirza, B., Ahmed, I., & Waheed, M. T. (2019) · Genomics · doi:10.1016/j.ygeno.2019.04.010 · Cited by 198 · see citing works
Cunha, M. D. P., Duarte‐Neto, A. N., Pour, S. Z., Ortiz-Báez, A. S., Černý, J., Pereira, B. B. D. S., Braconi, C. T., Ho, Y.-L., Perondi, B., Sztajnbok, J., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-56650-1 · Cited by 199 · see citing works
A novel SARS-CoV-2 related coronavirus in bats from Cambodia
Delaune, D., Hul, V., Karlsson, E. A., Hassanin, A., Ou, T. P., Baidaliuk, A., Gámbaro, F., Prot, M., Tú, V. T., Chea, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26809-4 · Cited by 219 · see citing works
Beresford-Jones, B. S., Forster, S. C., Stares, M. D., Notley, G., Viciani, E., Browne, H. P., Boehmler, D. J., Soderholm, A. T., Kumar, N., Vervier, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.003 · Cited by 194 · see citing works
Delmont, T. O., Gaia, M., Hinsinger, D. D., Frémont, P., Vanni, C., Fernandez-Guerra, A., Eren, A. M., Kourlaiev, A., d'Agata, L., Clayssen, Q., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100123 · Cited by 173 · see citing works
Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
Gonçalves, D. J. P., Simpson, B. B., Ortiz, E. M., Shimizu, G. H., & Jansen, R. K. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.05.022 · Cited by 191 · see citing works
Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA
Koopal, B., Potocnik, A., Mutte, S. K., Aparicio-Maldonado, C., Lindhoud, S., Vervoort, J. J. M., Brouns, S. J. J., & Swarts, D. C. (2022) · Cell · doi:10.1016/j.cell.2022.03.012 · Cited by 191 · see citing works
SARS‐CoV‐2, the pandemic coronavirus: Molecular and structural insights
Kadam, S. B., Sukhramani, G. S., Bishnoi, P., Pable, A. A., & Barvkar, V. T. (2021) · Journal of Basic Microbiology · doi:10.1002/jobm.202000537 · Cited by 193 · see citing works
CeMbio - The Caenorhabditis elegans Microbiome Resource
Dirksen, P., Assié, A., Zimmermann, J., Zhang, F., Tietje, A.-M., Marsh, S., Félix, M., Shapira, M., Kaleta, C., Hinrich Schulenburg, Y., et al. (2020) · G3 Genes Genomes Genetics · doi:10.1534/g3.120.401309 · Cited by 189 · see citing works
The Prevalence and Impact of Model Violations in Phylogenetic Analysis
Naser-Khdour, S., Minh, B. Q., Zhang, W., Stone, E. A., & Lanfear, R. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz193 · Cited by 181 · see citing works
Self-citationFrantzeskakis, L., Kracher, B., Kusch, S., Maekawa‐Yoshikawa, M., Bauer, S., Pedersen, C., Spanu, P. D., Maekawa, T., Schulze‐Lefert, P., & Panstruga, R. (2018) · BMC Genomics · doi:10.1186/s12864-018-4750-6 · Cited by 186 · see citing works
- Authors
- Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S.
- Affiliations
- Commonwealth Scientific and Industrial Research Organisation (AU)
- Australian National University (AU)
- Corresponding author
- Jermiin, Lars S
- Venue
- Nature Methods
- Published
- 2017-05-08
- Volume
- 14
- Issue
- 6
- Pages
- 587-589
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC5453245
- OpenAlex
- W2614081736
- Cited by
- 18,449
- References
- 38
- Citations by year
- 2026: 3177 · 2025: 3301 · 2024: 3175 · 2023: 2566 · 2022: 2243 · 2021: 1842 · 2020: 1156 · 2019: 672 · 2018: 271 · 2017: 34 · 2012: 2
- FWCI
- 238.81
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- model selection, phylogenetic inference, site rate heterogeneity, substitution models, model space search
- MeSH terms
- Algorithms, Animals, Chromosome Mapping, Computer Simulation, Humans, Models, Genetic, Phylogeny, Sensitivity and Specificity, Reproducibility of Results, Models, Statistical, Sequence Analysis, DNA, Evolution, Molecular, High-Throughput Nucleotide Sequencing
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