A new method for calculating evolutionary substitution rates

Evolution of Protein Molecules

JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032

Complete sequence of bovine mitochondrial DNA conserved features of the mammalian mitochondrial genome

Anderson, S., de Bruijn, M. H. L., Coulson, A. R., Eperon, I. C., Sanger, F., & Young, I. G. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90137-1 · Cited by 1,472

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

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

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 12,919

Ultrafast Approximation for Phylogenetic Bootstrap

Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst024 · Cited by 4,844

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

Chernomor, O., von Haeseler, A., & Minh, B. Q. (2016) · Systematic Biology · doi:10.1093/sysbio/syw037 · Cited by 2,252

The general stochastic model of nucleotide substitution

Rodríguez, F., Oliver, J. L., Marín, A., & Medina, J. R. (1990) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(05)80104-3 · Cited by 2,324

Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection

Kosakovsky Pond, S. L., & Frost, S. D. W. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi105 · Cited by 2,324

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

Criscuolo, A., & Gribaldo, S. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-210 · Cited by 1,633

Body size, metabolic rate, generation time, and the molecular clock.

Martin, A. P., & Palumbi, S. R. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.9.4087 · Cited by 1,239

Resolving difficult phylogenetic questions: Why more sequences are not enough

Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129

Estimating the pattern of nucleotide substitution

Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178256 · Cited by 1,076

Phylogeny Estimation and Hypothesis Testing Using Maximum Likelihood

Huelsenbeck, J. P., & Crandall, K. A. (1997) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.28.1.437 · Cited by 1,018

Recovering evolutionary trees under a more realistic model of sequence evolution.

(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040136 · Cited by 960

SIMMAP: Stochastic character mapping of discrete traits on phylogenies

Bollback, J. P. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-88 · Cited by 940

Increased Taxon Sampling Greatly Reduces Phylogenetic Error

Zwickl, D. J., & Hillis, D. M. (2002) · Systematic Biology · doi:10.1080/10635150290102339 · Cited by 939

Statistical tests of models of DNA substitution

Goldman, N. (1993) · Journal of Molecular Evolution · doi:10.1007/bf00166252 · Cited by 736

Bayesian random local clocks, or one rate to rule them all

Drummond, A. J., & Suchard, M. A. (2010) · BMC Biology · doi:10.1186/1741-7007-8-114 · Cited by 429

The Complete Sequence of the Zebrafish (Danio rerio) Mitochondrial Genome and Evolutionary Patterns in Vertebrate Mitochondrial DNA

Broughton, R. E., Milam, J. E., & Roe, B. A. (2001) · Genome Research · doi:10.1101/gr.156801 · Cited by 377

The importance of proper model assumption in bayesian phylogenetics.

Lemmon, A. R., & Moriarty, E. C. (2004) · Systematic Biology · doi:10.1080/10635150490423520 · Cited by 356

Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils

Schirrmeister, B. E., Gugger, M., & Donoghue, P. C. J. (2015) · Palaeontology · doi:10.1111/pala.12178 · Cited by 304

Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage

Hailer, F., Kutschera, V. E., Hallström, B. M., Klassert, D., Fain, S. R., Leonard, J. A., Arnason, U., & Janke, A. (2012) · Science · doi:10.1126/science.1216424 · Cited by 308

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., Wörheide, G., & Pisani, D. (2017) · Current Biology · doi:10.1016/j.cub.2017.11.008 · Cited by 291

Statistics and Truth in Phylogenomics

Kumar, S., Filipski, A. J., Battistuzzi, F. U., Kosakovsky Pond, S. L., & Tamura, K. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr202 · Cited by 287

Models of Molecular Evolution and Phylogeny: Table 1.

Liò, P., & Goldman, N. (1998) · Genome Research · doi:10.1101/gr.8.12.1233 · Cited by 284

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

Krause, J., Unger, T., Noçon, A., Malaspinas, A.-S., Kolokotronis, S.-O., Stiller, M., Soibelzon, L., Spriggs, H., Dear, P. H., Briggs, A. W., et al. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-220 · Cited by 284

The evolution of early Foraminifera

Pawlowski, J., Holzmann, M., Berney, C., Fahrni, J., Gooday, A. J., Cedhagen, T., Habura, A., & Bowser, S. S. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2035132100 · Cited by 275

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

Schierwater, B., Eitel, M., Jakob, W., Osigus, H.-J., Hadrys, H., Dellaporta, S. L., Kolokotronis, S.-O., & DeSalle, R. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000020 · Cited by 260

Parallel adaptations to high temperatures in the Archaean eon

Boussau, B., Blanquart, S., Necsulea, A., Lartillot, N., & Gouy, M. (2008) · Nature · doi:10.1038/nature07393 · Cited by 242

Adaptation to different human populations by HIV-1 revealed by codon-based analyses

Kosakovsky Pond, S. L., Frost, S. D. W., Grossman, Z., Gravenor, M. B., Richman, D. D., & Brown, A. J. L. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020062 · Cited by 223

Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters

Jeewon, R. (2002) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00422-0 · Cited by 209

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

Torruella, G., Derelle, R., Paps, J., Lang, B. F., Roger, A. J., Shalchian-Tabrizi, K., & Ruiz-Trillo, I. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr185 · Cited by 169

Pitfalls in supermatrix phylogenomics

Philippe, H., Vienne, D. M. D., Ranwez, V., Roure, B., Baurain, D., & Delsuc, F. (2017) · European Journal of Taxonomy · doi:10.5852/ejt.2017.283 · Cited by 173

Biased gene transfer in microbial evolution

Andam, C. P., & Gogarten, J. P. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2593 · Cited by 172

Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study

Rota-Stabelli, O., Lartillot, N., Philippe, H., & Pisani, D. (2013) · Systematic Biology · doi:10.1093/sysbio/sys077 · Cited by 155

Phylogeny and evolution of glass sponges (Porifera, Hexactinellida)

Dohrmann, M., Janussen, D., Reitner, J., Collins, A. G., & Wörheide, G. (2008) · Systematic Biology · doi:10.1080/10635150802161088 · Cited by 143

A new perspective on lower metazoan relationships from 18S rDNA sequences

Kim, J., Kim, W., & Cunningham, C. W. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026124 · Cited by 143

Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA

Bayha, K. M., Dawson, M. N., Collins, A. G., Barbeitos, M. S., & Haddock, S. H. D. (2010) · Integrative and Comparative Biology · doi:10.1093/icb/icq074 · Cited by 102

Local Molecular Clocks in Three Nuclear Genes: Divergence Times for Rodents and Other Mammals and Incompatibility Among Fossil Calibrations

Douzery, E. J. P., Delsuc, F., Stanhope, M. J., & Huchon, D. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-003-0028-x · Cited by 102

Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders.

HASEGAWA, M., & KISHINO, H. (1989) · The Japanese Journal of Genetics · doi:10.1266/jjg.64.243 · Cited by 71

Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan

Wei, L.-H., Yan, S., Lu, Y., Wen, S.-Q., Huang, Y.-Z., Wang, L.-X., Li, S.-L., Yang, Y.-J., Wang, X.-F., Zhang, C., et al. (2018) · European Journal of Human Genetics · doi:10.1038/s41431-017-0012-3 · Cited by 57

Rooting a phylogenetic tree with nonreversible substitution models.

Yap, V. B., & Speed, T. (2005) · BMC Evolutionary Biology · doi:10.1186/1471-2148-5-2 · Cited by 44