Evolution of Protein Molecules

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

WATSON, J. D., & CRICK, F. H. C. (1953) · Nature · doi:10.1038/171737a0 · Cited by 13,584 · see citing works

Gene Mutations in Human Hæmoglobin: the Chemical Difference Between Normal and Sickle Cell Hæmoglobin

INGRAM, V. M. (1957) · Nature · doi:10.1038/180326a0 · Cited by 978 · see citing works

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778 · see citing works

MODELTEST: 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

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 · see citing works

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 · see citing works

Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

Posada, D., & Buckley, T. R. (2004) · Systematic Biology · doi:10.1080/10635150490522304 · Cited by 3,927 · see citing works

ConSurf 2016: An improved methodology to estimate and visualize evolutionary conservation in macromolecules

Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., & Ben-Tal, N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw408 · Cited by 3,163 · see citing works

The Human Oral Microbiome

Dewhirst, F. E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C. R., Yu, W.-H., Lakshmanan, A., & Wade, W. G. (2010) · Journal of Bacteriology · doi:10.1128/jb.00542-10 · Cited by 3,352 · see citing works

Defining the normal bacterial flora of the oral cavity

Aas, J. A., Paster, B. J., Stokes, L. N., Olsen, I., & Dewhirst, F. E. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.11.5721-5732.2005 · Cited by 3,092 · see citing works

Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies

Strimmer, K., & von Haeseler, A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025664 · Cited by 2,531 · see citing works

Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters

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Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

Davydov, E. V., Goode, D. L., Sirota, M., Cooper, G. M., Sidow, A., & Batzoglou, S. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001025 · Cited by 1,757 · see citing works

Mitochondrial DNA sequences of primates: tempo and mode of evolution

Brown, W. M., Prager, E. M., Wang, A., & Wilson, A. C. (1982) · Journal of Molecular Evolution · doi:10.1007/bf01734101 · Cited by 1,554 · see citing works

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., et al. (2021) · Science · doi:10.1126/science.abh2644 · Cited by 1,461 · see citing works

Bayesian species delimitation using multilocus sequence data

Yang, Z., & Rannala, B. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913022107 · Cited by 1,405 · see citing works

Estimating the rate of evolution of the rate of molecular evolution

Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317 · see citing works

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 · see citing works

<i>Yersinia pestis</i> , the cause of plague, is a recently emerged clone of <i>Yersinia pseudotuberculosis</i>

Achtman, M., Zurth, K., Morelli, G., Torrea, G., Guiyoule, A., & Carniel, E. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.24.14043 · Cited by 1,126 · see citing works

Estimating the pattern of nucleotide substitution

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

Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals

Lovley, D. R., Giovannoni, S. J., White, D. C., Champine, J. E., Phillips, E. J. P., Gorby, Y. A., & Goodwin, S. (1993) · Archives of Microbiology · doi:10.1007/bf00290916 · Cited by 983 · see citing works

Divergence time and evolutionary rate estimation with multilocus data.

Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962 · see citing works

Bacteria of Dental Caries in Primary and Permanent Teeth in Children and Young Adults

Aas, J. A., Griffen, A. L., Dardis, S. R., Lee, A. M., Olsen, I., Dewhirst, F. E., Leys, E. J., & Paster, B. J. (2008) · Journal of Clinical Microbiology · doi:10.1128/jcm.01410-07 · Cited by 952 · see citing works

Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism

Caccavo, F., Lonergan, D. J., Lovley, D. R., Davis, M., Stolz, J. F., & McInerney, M. J. (1994) · Applied and Environmental Microbiology · doi:10.1128/aem.60.10.3752-3759.1994 · Cited by 896 · see citing works

Subtilases: the superfamily of subtilisin-like serine proteases.

Siezen, R. J., & Leunissen, J. A. M. (1997) · Protein Science · doi:10.1002/pro.5560060301 · Cited by 896 · see citing works

Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models

Suchard, M. A., Weiss, R. E., & Sinsheimer, J. S. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003872 · Cited by 791 · see citing works

Candida dubliniensis sp. nov.: phenotypic and molecular characterization of a novel species associated with oral candidosis in HIV-infected individuals

Sullivan, D. J., Haynes, K. A., Bennett, D. E., Coleman, D. C., & Westerneng, T. J. (1995) · Microbiology · doi:10.1099/13500872-141-7-1507 · Cited by 763 · see citing works

Statistical tests of models of DNA substitution

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

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

Lartillot, N., Brinkmann, H., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s4 · Cited by 705 · see citing works

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome

Saulnier, D. M., Riehle, K., Mistretta, T., Diaz, M., Mandal, D., Raza, S., Weidler, E. M., Qin, X., Coarfa, C., Milosavljevic, A., et al. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.06.072 · Cited by 672 · see citing works

Missing Data, Incomplete Taxa, and Phylogenetic Accuracy

Wiens, J. J. (2003) · Systematic Biology · doi:10.1080/10635150390218330 · Cited by 691 · see citing works

Performance of a divergence time estimation method under a probabilistic model of rate evolution.

Kishino, H., Thorne, J. L., & Bruno, W. J. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003811 · Cited by 633 · see citing works

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586 · see citing works

Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock

Doolittle, R. F., Feng, D.-F., Tsang, S., Cho, G., & Little, E. (1996) · Science · doi:10.1126/science.271.5248.470 · Cited by 581 · see citing works

Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria

Berman-Frank, I., Lundgren, P., & Falkowski, P. (2003) · Research in Microbiology · doi:10.1016/s0923-2508(03)00029-9 · Cited by 522 · see citing works

Modeling compositional heterogeneity

Foster, P. G. (2004) · Systematic Biology · doi:10.1080/10635150490445779 · Cited by 474 · see citing works

Total-Evidence Dating under the Fossilized Birth–Death Process

Zhang, C., Stadler, T., Klopfstein, S., Heath, T. A., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syv080 · Cited by 419 · see citing works

Model Selection in Phylogenetics

Sullivan, J., & Joyce, P. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.36.102003.152633 · Cited by 412 · see citing works

Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria

Lonergan, D. J., Jenter, H. L., Coates, J. D., Phillips, E. J., Schmidt, T. M., & Lovley, D. R. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.8.2402-2408.1996 · Cited by 380 · see citing works

Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer

Coates, J. D., Ellis, D. J., Gaw, C. V., & Lovley, D. R. (1999) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/00207713-49-4-1615 · Cited by 382 · see citing works

The molecular clock runs more slowly in man than in apes and monkeys

Li, W.-H., & Tanimura, M. (1987) · Nature · doi:10.1038/326093a0 · Cited by 375 · see citing works

Application of Novel PCR-Based Methods for Detection, Quantitation, and Phylogenetic Characterization of <i>Sutterella</i> Species in Intestinal Biopsy Samples from Children with Autism and Gastrointestinal Disturbances

Williams, B. L., Hornig, M., Parekh, T., & Lipkin, W. I. (2012) · mBio · doi:10.1128/mbio.00261-11 · Cited by 378 · see citing works

A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data

Barker, F. K., Barrowclough, G. F., & Groth, J. G. (2002) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.2001.1883 · Cited by 377 · see citing works

Genome-Wide Inference of Ancestral Recombination Graphs

Rasmussen, M. D., Hubisz, M. J., Gronau, I., & Siepel, A. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004342 · Cited by 371 · see citing works

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 · see citing works

Comparison of Likelihood and Bayesian Methods for Estimating Divergence Times Using Multiple Gene Loci and Calibration Points, with Application to a Radiation of Cute-Looking Mouse Lemur Species

Yang, Z., & Yoder, A. D. (2003) · Systematic Biology · doi:10.1080/10635150390235557 · Cited by 357 · see citing works

Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes

Zhang, J. (2000) · Journal of Molecular Evolution · doi:10.1007/s002399910007 · Cited by 356 · see citing works

PHYLOGENETIC ANALYSIS IN MOLECULAR EVOLUTIONARY GENETICS

Nei, M. (1996) · Annual Review of Genetics · doi:10.1146/annurev.genet.30.1.371 · Cited by 349 · see citing works

Moderate mutation rate in the SARS coronavirus genome and its implications

Zhao, Z., Li, H., Wu, X., Zhong, Y., Zhang, K., Zhang, Y.-P., Boerwinkle, E., & Fu, Y.-X. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-21 · Cited by 286 · see citing works

Estimating divergence dates from molecular sequences.

Rambaut, A., & Bromham, L. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025940 · Cited by 298 · see citing works

Anaerobic Benzene Oxidation in the Fe(III) Reduction Zone of Petroleum-Contaminated Aquifers

Anderson, R. T., Rooney-Varga, J. N., Gaw, C. V., & Lovley, D. R. (1998) · Environmental Science &amp; Technology · doi:10.1021/es9704949 · Cited by 285 · see citing works

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Goldman, N., Thorne, J. L., & Jones, D. T. (1998) · Genetics · doi:10.1093/genetics/149.1.445 · Cited by 281 · see citing works

Model misspecification and probabilistic tests of topology: evidence from empirical data sets.

Buckley, T. R. (2002) · Systematic Biology · doi:10.1080/10635150290069922 · Cited by 253 · see citing works

Subgingival biodiversity in subjects with uncontrolled type‐2 diabetes and chronic periodontitis

Casarin, R. C. V., Barbagallo, A., Meulman, T., Santos, V. R., Sallum, E. A., Nociti, F. H., Duarte, P. M., Casati, M. Z., & Gonçalves, R. B. (2013) · Journal of Periodontal Research · doi:10.1111/j.1600-0765.2012.01498.x · Cited by 256 · see citing works

Bayesian Model Adequacy and Choice in Phylogenetics

Bollback, J. P. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004175 · Cited by 215 · see citing works

Consequences of Range Contractions and Range Shifts on Molecular Diversity

Arenas, M., Ray, N., Currat, M., & Excoffier, L. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr187 · Cited by 236 · see citing works

Inferring the root of a phylogenetic tree.

Huelsenbeck, J. P., Bollback, J. P., & Levine, A. M. (2002) · Systematic Biology · doi:10.1080/106351502753475862 · Cited by 221 · see citing works

Branch-length prior influences Bayesian posterior probability of phylogeny.

Yang, Z., & Rannala, B. (2005) · Systematic Biology · doi:10.1080/10635150590945313 · Cited by 228 · see citing works

Lactobacillus diolivorans sp. nov., a 1,2-propanediol-degrading bacterium isolated from aerobically stable maize silage.

Krooneman, J., Faber, F., Alderkamp, A. C., Elferink, S. J. H. W. O., Driehuis, F., Cleenwerck, I., Swings, J., Gottschal, J. C., & Vancanneyt, M. (2002) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/00207713-52-2-639 · Cited by 226 · see citing works

Dating primate divergences through an integrated analysis of palaeontological and molecular data

Wilkinson, R. D., Steiper, M. E., Soligo, C., Martin, R. D., Yang, Z., & Tavaré, S. (2011) · Systematic Biology · doi:10.1093/sysbio/syq054 · Cited by 218 · see citing works

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 · see citing works

Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation

Ho, S. Y. W. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi125 · Cited by 190 · see citing works

On Reduced Amino Acid Alphabets for Phylogenetic Inference

Susko, E., & Roger, A. J. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm144 · Cited by 177 · see citing works

Molecular analysis of oral and respiratory bacterial species associated with ventilator-associated pneumonia.

Bahrani-Mougeot, F. K., Paster, B. J., Coleman, S., Barbuto, S., Brennan, M. T., Noll, J., Kennedy, T., Fox, P. C., & Lockhart, P. B. (2007) · Journal of Clinical Microbiology · doi:10.1128/jcm.01963-06 · Cited by 176 · see citing works

Dating tips for divergence time estimation

O’Reilly, J. E., dos Reis, M., & Donoghue, P. C. J. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.08.001 · Cited by 159 · see citing works

Context Dependence, Ancestral Misidentification, and Spurious Signatures of Natural Selection

Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm108 · Cited by 169 · see citing works

Chrysiogenes arsenatis gen. nov., sp. nov., a New Arsenate-Respiring Bacterium Isolated from Gold Mine Wastewater

MACY, J. M., NUNAN, K., HAGEN, K. D., DIXON, D. R., HARBOUR, P. J., CAHILL, M., & SLY, L. I. (1996) · International Journal of Systematic Bacteriology · doi:10.1099/00207713-46-4-1153 · Cited by 164 · see citing works

Bayesian Models of Episodic Evolution Support a Late Precambrian Explosive Diversification of the Metazoa

Aris-Brosou, S. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg226 · Cited by 164 · see citing works

Phylogeny and systematics of 18 <i>Colletotrichum</i> species based on ribosomal DNA spacer sequences

Sreenivasaprasad, S., Meehan, B. M., Mills, P. R., & Brown, A. E. (1996) · Genome · doi:10.1139/g96-064 · Cited by 158 · see citing works

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

Moses, A. M., Chiang, D. Y., Pollard, D. A., Iyer, V. N., & Eisen, M. B. (2004) · Genome Biology · doi:10.1186/gb-2004-5-12-r98 · Cited by 153 · see citing works

The unbearable uncertainty of Bayesian divergence time estimation

DOS REIS, M., & YANG, Z. (2013) · Journal of Systematics and Evolution · doi:10.1111/j.1759-6831.2012.00236.x · Cited by 140 · see citing works

The rise and fall of African rice cultivation revealed by analysis of 246 new genomes

Cubry, P., Tranchant-Dubreuil, C., Thuillet, A.-C., Monat, C., Ndjiondjop, M.-N., Labadie, K., Cruaud, C., Engelen, S., Scarcelli, N., Rhoné, B., et al. (2018) · Current Biology · doi:10.1016/j.cub.2018.05.066 · Cited by 142 · see citing works

Rhodovulum iodosum sp. nov. and Rhodovulum robiginosum sp. nov., two new marine phototrophic ferrous-iron-oxidizing purple bacteria

Straub, K. L., Rainey, F. A., & Widdel, F. (1999) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-49-2-729 · Cited by 140 · see citing works

Correlated mutations in models of protein sequences: phylogenetic and structural effects

Lapedes, A. S., Giraud, B., Liu, L., & Stormo, G. D. (1999) · Institute of Mathematical Statistics Lecture Notes - Monograph Series · doi:10.1214/lnms/1215455556 · Cited by 124 · see citing works

Amphioxus homologs of Go‐coupled rhodopsin and peropsin having 11‐<i>cis</i>‐ and all‐<i>trans</i>‐retinals as their chromophores

Koyanagi, M., Terakita, A., Kubokawa, K., & Shichida, Y. (2002) · FEBS Letters · doi:10.1016/s0014-5793(02)03616-5 · Cited by 114 · see citing works

Trichuris suis and Trichuris trichiura are different nematode species

Cutillas, C., Callejón, R., de Rojas, M., Tewes, B., Ubeda, J. M., Ariza, C., & Guevara, D. C. (2009) · Acta Tropica · doi:10.1016/j.actatropica.2009.05.011 · Cited by 110 · see citing works

Rooting the tree of life: the phylogenetic jury is still out

Gouy, R., Baurain, D., & Philippe, H. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0329 · Cited by 96 · see citing works

Genetic diversity patterns of Haemonchus placei and Haemonchus contortus populations isolated from domestic ruminants in Brazil

Brasil, B. S. A. F., Nunes, R. L., Bastianetto, E., Drummond, M. G., Carvalho, D. C., Leite, R. C., Molento, M. B., & Oliveira, D. A. A. (2012) · International Journal for Parasitology · doi:10.1016/j.ijpara.2012.03.003 · Cited by 106 · see citing works

The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci

Dos Reis, M., Zhu, T., & Yang, Z. (2014) · Systematic Biology · doi:10.1093/sysbio/syu020 · Cited by 93 · see citing works

Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites

Adachi, J., & Hasegawa, M. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00160510 · Cited by 94 · see citing works

Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci

Zhu, T., Dos Reis, M., & Yang, Z. (2015) · Systematic Biology · doi:10.1093/sysbio/syu109 · Cited by 86 · see citing works

<scp>POY</scp> version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria

Wheeler, W. C., Lucaroni, N., Hong, L., Crowley, L. M., & Varón, A. (2015) · Cladistics · doi:10.1111/cla.12083 · Cited by 89 · see citing works

Serial Recombination during Circulation of Type 1 Wild-Vaccine Recombinant Polioviruses in China

Liu, H.-M., Zheng, D.-P., Zhang, L.-B., Oberste, M. S., Kew, O. M., & Pallansch, M. A. (2003) · Journal of Virology · doi:10.1128/jvi.77.20.10994-11005.2003 · Cited by 88 · see citing works

An Estimate of Divergence Time of Parazoa and Eumetazoa and That of Cephalochordata and Vertebrata by Aldolase and Triose Phosphate Isomerase Clocks

Nikoh, N., Iwabe, N., Kuma, K.-I., Ohno, M., Sugiyama, T., Watanabe, Y., Yasui, K., Shi-cui, Z., Hori, K., Shimura, Y., et al. (1997) · Journal of Molecular Evolution · doi:10.1007/pl00006208 · Cited by 79 · see citing works

Profiling bacterial community in upper respiratory tracts

Yi, H., Yong, D., Lee, K., Cho, Y.-J., & Chun, J. (2014) · BMC Infectious Diseases · doi:10.1186/s12879-014-0583-3 · Cited by 75 · see citing works

Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria

Sghaier, H., Ghedira, K., Benkahla, A., & Barkallah, I. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-297 · Cited by 71 · see citing works

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

Roure, B., & Philippe, H. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-17 · Cited by 64 · see citing works

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses

Polavarapu, N., Bowen, N. J., & McDonald, J. F. (2006) · Genome Biology · doi:10.1186/gb-2006-7-6-r51 · Cited by 60 · see citing works

Scalable empirical mixture models that account for across-site compositional heterogeneity

Schrempf, D., Lartillot, N., & Szöllősi, G. (2019) · doi:10.1101/794263 · Cited by 61 · see citing works

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 · see citing works

Assessment of substitution model adequacy using frequentist and Bayesian methods

Ripplinger, J., & Sullivan, J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq168 · Cited by 50 · see citing works

Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

Pervez, M. T., Babar, M. E., Nadeem, A., Aslam, M., Awan, A. R., Aslam, N., Hussain, T., Naveed, N., Qadri, S., Waheed, U., et al. (2014) · Evolutionary Bioinformatics · doi:10.4137/ebo.s19199 · Cited by 48 · see citing works

SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal

Currat, M., Arenas, M., Quilodràn, C. S., Excoffier, L., & Ray, N. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz311 · Cited by 47 · see citing works

PopHuman: the human population genomics browser

Casillas, S., Mulet, R., Villegas-Mirón, P., Hervas, S., Sanz, E., Velasco, D., Bertranpetit, J., Laayouni, H., & Barbadilla, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx943 · Cited by 29 · see citing works

Biogeographical distribution of<i>Rimicaris exoculata</i>resident gut epibiont communities along the Mid-Atlantic Ridge hydrothermal vent sites

Durand, L., Roumagnac, M., Cueff-Gauchard, V., Jan, C., Guri, M., Tessier, C., Haond, M., Crassous, P., Zbinden, M., Arnaud-Haond, S., et al. (2015) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiv101 · Cited by 32 · see citing works

Taxonomic revision of commercially used<i>Arthrospira</i>(Cyanobacteria) strains: a polyphasic approach

Papapanagiotou, G., & Gkelis, S. (2019) · European Journal of Phycology · doi:10.1080/09670262.2019.1624832 · Cited by 26 · see citing works

From epigenotype to new genotypes: Relevance of epigenetic mechanisms in the emergence of genomic evolutionary novelty

Guerrero-Bosagna, C. (2020) · Seminars in Cell &amp; Developmental Biology · doi:10.1016/j.semcdb.2019.07.006 · Cited by 26 · see citing works

Phylogenetic relationships of Arthrospira strains inferred from 16S rRNA gene and cpcBA-IGS sequences

Choi, G.-G., Ahn, C.-Y., & Oh, H.-M. (2012) · ALGAE · doi:10.4490/algae.2012.27.2.075 · Cited by 18 · see citing works

Prevalence and phylogenetic analysis of Babesia spp. in Ixodes ricinus and Ixodes persulcatus ticks in Latvia

Capligina, V., Berzina, I., Bormane, A., Salmane, I., Vilks, K., Kazarina, A., Bandere, D., Baumanis, V., & Ranka, R. (2016) · Experimental and Applied Acarology · doi:10.1007/s10493-015-9978-0 · Cited by 21 · see citing works

On the dispersion index of a Markovian molecular clock

Zheng, Q. (2001) · Mathematical Biosciences · doi:10.1016/s0025-5564(01)00067-0 · Cited by 17 · see citing works

The identification and functional implications of human-specific “fixed” amino acid substitutions in the glutamate receptor family

Goto, H., Watanabe, K., Araragi, N., Kageyama, R., Tanaka, K., Kuroki, Y., Toyoda, A., Hattori, M., Sakaki, Y., Fujiyama, A., et al. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-224 · Cited by 16 · see citing works

Relative Time Constraints Improve Molecular Dating

Szöllõsi, G. J., Höhna, S., Williams, T. A., Schrempf, D., Daubin, V., & Boussau, B. (2022) · Systematic Biology · doi:10.1093/sysbio/syab084 · Cited by 23 · see citing works