RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

MrBayes 3: Bayesian phylogenetic inference under mixed models

Ronquist, F., & Huelsenbeck, J. P. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg180 · Cited by 29,194

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,923

Obesity alters gut microbial ecology

Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176

Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion

Zwickl, D. J. (2006) · Texas ScholarWorks (Texas Digital Library) · Cited by 3,108

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

Stamatakis, A., Ludwig, T. G., & Meier, H. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti191 · Cited by 1,429

Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat

Ley, R. E., Harris, J. K., Wilcox, J., Spear, J. R., Miller, S. R., Bebout, B. M., Maresca, J. A., Bryant, D. A., Sogin, M. L., & Pace, N. R. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.5.3685-3695.2006 · Cited by 472

Phylogenetic models of rate heterogeneity: A high performance computing perspective

Stamatakis, A. (2006) · Cited by 303

Phylogenetic models of rate heterogeneity: a high performance computing perspective

Stamatakis, A. (2006) · IEEE International Parallel and Distributed Processing Symposium (IPDPS) · doi:10.1109/ipdps.2006.1639535 · Cited by 292

Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood

Hordijk, W., & Gascuel, O. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti713 · Cited by 213

Phylogenetic diversity and ecology of environmental Archaea

Robertson, C. E., Harris, J. K., Spear, J. R., & Pace, N. R. (2005) · Current Opinion in Microbiology · doi:10.1016/j.mib.2005.10.003 · Cited by 155

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

Singh, R., Ong‐Abdullah, M., Low, E. L., Manaf, M. A. A., Rosli, R., Nookiah, R., Ooi, L. C., Ooi, S., Chan, K., Halim, M. A. A., et al. (2013) · Nature · doi:10.1038/nature12309 · Cited by 626

A class-wide phylogenetic assessment of Dothideomycetes

Schoch, C. L., Crous, P. W., Groenewald, J. Z., Boehm, E. W. A., Burgess, T. I., de Gruyter, J., de Hoog, S., Dixon, L. J., Grube, M., Gueidan, C., et al. (2009) · Studies in Mycology · doi:10.3114/sim.2009.64.01 · Cited by 624

Inferring ancient divergences requires genes with strong phylogenetic signals

Salichos, L., & Rokas, A. (2013) · Nature · doi:10.1038/nature12130 · Cited by 616

An environmental bacterial taxon with a large and distinct metabolic repertoire

Wilson, M. C., Mori, T., Rückert, C., Uria, A. R., Helf, M. J., Takada, K., Gernert, C., Steffens, U. A. E., Heycke, N., Schmitt, S., et al. (2014) · Nature · doi:10.1038/nature12959 · Cited by 612

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

Green, R. E., Malaspinas, A., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maričić, T., Stenzel, U., et al. (2008) · Cell · doi:10.1016/j.cell.2008.06.021 · Cited by 608

The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life

Jetz, W., & Pyron, R. A. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0515-5 · Cited by 607

Establishment of Characteristic Gut Bacteria during Development of the Honeybee Worker

Martinson, V. G., Moy, J. K., & Moran, N. A. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.07810-11 · Cited by 605

A simple and distinctive microbiota associated with honey bees and bumble bees

Martinson, V. G., Danforth, B. N., Minckley, R. L., Rueppell, O., Tingek, S., & Moran, N. A. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04959.x · Cited by 601

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Weyrich, L. S., Duchêne, S., Soubrier, J., Arriola, L. A., Llamas, B., Breen, J., Morris, A. G., Alt, K. W., Caramelli, D., Dresely, V., et al. (2017) · Nature · doi:10.1038/nature21674 · Cited by 599

Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium

Bryant, J. M., Grogono, D., Rodriguez-Rincon, D., Everall, I., Brown, K., Moreno, P. A., Verma, D., Hill, E. M., Drijkoningen, J., Gilligan, P. H., et al. (2016) · Science · doi:10.1126/science.aaf8156 · Cited by 596

ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences

Lee, I., Chalita, M., Ha, S. M., Na, S.-I., Yoon, S.-H., & Chun, J. (2017) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.001872 · Cited by 587

Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions

Graf, D. R. H., Jones, C. M., & Hallin, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0114118 · Cited by 583

Detecting hidden diversification shifts in models of trait-dependent speciation and extinction

Beaulieu, J. M., & O’Meara, B. C. (2016) · Systematic Biology · doi:10.1093/sysbio/syw022 · Cited by 579

Ensembl comparative genomics resources

Herrero, J., Muffato, M., Beal, K. M., Fitzgerald, S. F., Gordon, L., Pignatelli, M., Vilella, A. J., Searle, S. M. J., Amode, R., Brent, S., et al. (2016) · Database · doi:10.1093/database/bav096 · Cited by 583

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

Neafsey, D. E., Waterhouse, R. M., Abai, M. R., Aganezov, S. S., Alekseyev, M. A., Allen, J. E., Amon, J., Arcà, B., Arensburger, P., Николаевич, А. Г., et al. (2014) · Science · doi:10.1126/science.1258522 · Cited by 573

Global dissemination of a multidrug resistant Escherichia coli clone

Petty, N. K., Zakour, N. L. B., Stanton-Cook, M. J., Skippington, E., Totsika, M., Forde, B. M., Phan, M., Moriel, D. G., Peters, K. M., Davies, M. R., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1322678111 · Cited by 571

Patterns of Rare and Abundant Marine Microbial Eukaryotes

Logares, R., Audic, S., Bass, D., Bittner, L., Boutte, C., Christen, R., Claverie, J., Decelle, J., Dolan, J. R., Dunthorn, M., et al. (2014) · Current Biology · doi:10.1016/j.cub.2014.02.050 · Cited by 569

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

Malinsky, M., Svardal, H., Tyers, A. M., Miska, E. A., Genner, M. J., Turner, G. F., & Durbin, R. M. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0717-x · Cited by 568

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

Schubert, M., Ermini, L., Sarkissian, C. D., Jónsson, H., Ginolhac, A., Schaefer, R., Martin, M. D., Fernández, R., Kircher, M., McCue, M., et al. (2014) · Nature Protocols · doi:10.1038/nprot.2014.063 · Cited by 562

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Rouxel, T., Grandaubert, J., Hane, J. K., Hoede, C., de Wouw, A. P. V., Couloux, A., Angel, V. D. D., Anthouard, V., Bally, P., Bourras, S., et al. (2011) · Nature Communications · doi:10.1038/ncomms1189 · Cited by 561

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

Särkinen, T., Bohs, L., Olmstead, R. G., & Knapp, S. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-214 · Cited by 560

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

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 560

Taxon sampling and the accuracy of phylogenetic analyses

(2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08016 · Cited by 553

Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses

Liu, D., Shi, W., Shi, Y., Wang, D., Xiao, H., Li, W., Bi, Y., Wu, Y., Li, X., Yan, J., et al. (2013) · The Lancet · doi:10.1016/s0140-6736(13)60938-1 · Cited by 553

FASconCAT: Convenient handling of data matrices

Kück, P., & Meusemann, K. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.04.024 · Cited by 550

Contemporaneous and recent radiations of the world's major succulent plant lineages

Arakaki, M., Christin, P., Nyffeler, R., Lendel, A., Eggli, U., Ogburn, R. M., Spriggs, E. L., Moore, M. J., & Edwards, E. J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100628108 · Cited by 544

ALTER: program-oriented conversion of DNA and protein alignments

Glez‐Peña, D., mez-Blanco, D. G. ⁄., Reboiro‐Jato, M., Fdez‐Riverola, F., & Posada, D. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq321 · Cited by 542

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

Kembel, S. W., Wu, M., Eisen, J. A., & Green, J. L. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002743 · Cited by 542

amoA ‐based consensus phylogeny of ammonia‐oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

Pester, M., Rattei, T., Flechl, S., Gröngröft, A., Richter, A. A., Overmann, J., Reinhold‐Hurek, B., Loy, A., & Wagner, M. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02666.x · Cited by 542

A renaissance for the pioneering 16S rRNA gene

Tringe, S. G., & Hugenholtz, P. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.011 · Cited by 540

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice

(2014) · doi:10.1007/978-3-662-43550-2 · Cited by 538

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M., Richter, R. A., Valas, R. E., Novotny, M. A., Yee-Greenbaum, J. L., Selengut, J., Haft, D. H., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.189 · Cited by 538

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.01.014 · Cited by 536

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

Allen, A. E., Dupont, C. L., Obornı́k, M., Horák, A., Nunes‐Nesi, A., McCrow, J. P., Zheng, H., Johnson, D. A., Hu, H., Fernie, A. R., et al. (2011) · Nature · doi:10.1038/nature10074 · Cited by 536

Identification of Klebsiella capsule synthesis loci from whole genome data

Wyres, K. L., Wick, R. R., Gorrie, C. L., Jenney, A. W. J., Follador, R., Thomson, N. R., & Holt, K. E. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000102 · Cited by 536

The beetle tree of life reveals that C oleoptera survived end‐ P ermian mass extinction to diversify during the C retaceous terrestrial revolution

McKenna, D. D., Wild, A. L., Kanda, K., Bellamy, C. L., BEUTEL, R. G., Caterino, M. S., FARNUM, C. W., Hawks, D. C., Ivie, M. A., Jameson, M. L., et al. (2015) · Systematic Entomology · doi:10.1111/syen.12132 · Cited by 530

Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

Angel, R., Claus, P., & Conrad, R. (2011) · The ISME Journal · doi:10.1038/ismej.2011.141 · Cited by 529

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

Eaton, D. A. R., & Ree, R. H. (2013) · Systematic Biology · doi:10.1093/sysbio/syt032 · Cited by 526

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2693 · Cited by 524

A glimpse on the pattern of rodent diversification: a phylogenetic approach

Fabre, P., Hautier, L., Dimitrov, D., & Douzery, E. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-88 · Cited by 521

A genome triplication associated with early diversification of the core eudicots

Jiao, Y., Leebens‐Mack, J., Ayyampalayam, S., Bowers, J., McKain, M. R., McNeal, J. R., Rolf, M., Ruzicka, D. R., Wafula, E. K., Wickett, N. J., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-1-r3 · Cited by 520

A simple, fast, and accurate method of phylogenomic inference

Wu, M., & Eisen, J. A. (2008) · Genome biology · doi:10.1186/gb-2008-9-10-r151 · Cited by 519

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

Simion, P., Philippe, H., Baurain, D., Jager, M., Richter, D. J., Di Franco, A., Roure, B., Satoh, N., Quéinnec, É., Ereskovsky, A., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.02.031 · Cited by 518

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Miyauchi, S., Kiss, E., Kuo, A., Drula, É., Kohler, A., Sánchez‐García, M., Morin, E., Andreopoulos, B., Barry, K., Bonito, G. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18795-w · Cited by 518

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

Berger, S. A., Krompaß, D., & Stamatakis, A. (2011) · Systematic Biology · doi:10.1093/sysbio/syr010 · Cited by 515

Comparative Genomics of the Odorant-Binding and Chemosensory Protein Gene Families across the Arthropoda: Origin and Evolutionary History of the Chemosensory System

Vieira, F. G., & Rozas, J. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr033 · Cited by 515

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

Liu, K., Raghavan, S., Nelesen, S. M., Linder, C. R., & Warnow, T. J. (2009) · Science · doi:10.1126/science.1171243 · Cited by 509

New grass phylogeny resolves deep evolutionary relationships and discovers C 4 origins

Grass Phylogeny Working Group II (2011) · New Phytologist · doi:10.1111/j.1469-8137.2011.03972.x · Cited by 507

Human papillomavirus genome variants

Burk, R. D., Harari, A., & Chen, Z. (2013) · Virology · doi:10.1016/j.virol.2013.07.018 · Cited by 504

Ecological opportunity and sexual selection together predict adaptive radiation

Wagner, C. E., Harmon, L. J., & D, O. S. C. (2012) · Nature · doi:10.1038/nature11144 · Cited by 502

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Near, T. J., Dornburg, A., Eytan, R. I., Keck, B. P., Smith, W. L., Kuhn, K. L., Moore, J. A., Price, S. A., Burbrink, F. T., Friedman, M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1304661110 · Cited by 502

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

Bertels, F., Silander, O., Pachkov, M. V., Rainey, P. B., & van Nimwegen, E. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu088 · Cited by 501

Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes

Skippington, E., Barkman, T. J., Rice, D. W., & Palmer, J. D. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1504491112 · Cited by 499

Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status

Tonini, J. F. R., Beard, K. H., Ferreira, R. B., Jetz, W., & Pyron, R. A. (2016) · Biological Conservation · doi:10.1016/j.biocon.2016.03.039 · Cited by 499

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Nyakatura, K., & Bininda‐Emonds, O. R. P. (2012) · BMC Biology · doi:10.1186/1741-7007-10-12 · Cited by 493

Species Delimitation using Genome-Wide SNP Data

Leaché, A. D., Fujita, M. K., Minin, V. N., & Bouckaert, R. (2014) · Systematic Biology · doi:10.1093/sysbio/syu018 · Cited by 493

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Li, F., Brouwer, P., Carretero‐Paulet, L., Cheng, S., de Vries, J., Delaux, P., Eily, A. N., Koppers, N., Kuo, L., Li, Z., et al. (2018) · Nature Plants · doi:10.1038/s41477-018-0188-8 · Cited by 492

Phylogenomics reveals deep molluscan relationships

Kocot, K. M., Cannon, J. T., Todt, C., Citarella, M. R., Kohn, A. B., Meyer, A., Santos, S. R., Schänder, C., Moroz, L. L., Lieb, B., et al. (2011) · Nature · doi:10.1038/nature10382 · Cited by 491

A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids

Janouškovec, J., Horák, A., Oborník, M., Lukeš, J., & Keeling, P. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1003335107 · Cited by 489

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”

Hampl, V., Hug, L. A., Leigh, J., Dacks, J. B., Lang, B. F., Simpson, A. G. B., & Roger, A. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807880106 · Cited by 488

A single mutation in the prM protein of Zika virus contributes to fetal microcephaly

Yuan, L., Huang, X., Liu, Z., Zhang, F., Zhu, X., Yu, J.-Y., Ji, X., Xu, Y., Li, G., Li, C., et al. (2017) · Science · doi:10.1126/science.aam7120 · Cited by 482

Fungi vs. Fungi in Biocontrol: An Overview of Fungal Antagonists Applied Against Fungal Plant Pathogens

Thambugala, K. M., Daranagama, D. A., Phillips, A. J. L., Kannangara, S. D., & Promputtha, I. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.604923 · Cited by 478

Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

Lebreton, F., van Schaik, W., Manson, A. L., Godfrey, P. A., Griggs, A. D., Mazumdar, V., Corander, J., Cheng, L., Saif, S., Young, S., et al. (2013) · mBio · doi:10.1128/mbio.00534-13 · Cited by 476

Fungal diversity notes 1–110: taxonomic and phylogenetic contributions to fungal species

Liu, J., Hyde, K. D., Jones, E. B. G., Ariyawansa, H. A., Bhat, D. J., Boonmee, S., Maharachchikumbura, S. S. N., McKenzie, E. H. C., Phookamsak, R., Phukhamsakda, C., et al. (2015) · Fungal Diversity · doi:10.1007/s13225-015-0324-y · Cited by 476

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

Wong, V., Baker, S. G., Pickard, D., Parkhill, J., Page, A. J., Feasey, N., Kingsley, R. A., Thomson, N. R., Keane, J. A., Weill, F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3281 · Cited by 473

The genesis and source of the H7N9 influenza viruses causing human infections in China

Lam, T. T., Wang, J., Shen, Y., Zhou, B., Duan, L., Cheung, C.-L., Ma, C., Lycett, S., Leung, C. Y. H., Chen, X., et al. (2013) · Nature · doi:10.1038/nature12515 · Cited by 473

Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes

Schuettpelz, E., & Pryer, K. M. (2007) · Taxon · doi:10.2307/25065903 · Cited by 472

The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

Fritz‐Laylin, L. K., Prochnik, S. E., Ginger, M. L., Dacks, J. B., Carpenter, M. L., Field, M. C., Kuo, A., Paredez, A. R., Chapman, J., Pham, J. K., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.032 · Cited by 472

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Song, S., Liu, L., Edwards, S. V., & Wu, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211733109 · Cited by 472

AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential

Alanjary, M. M., Steinke, K., & Ziemert, N. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz282 · Cited by 472

Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics

Weitemier, K., Straub, S. C. K., Cronn, R., Fishbein, M., Schmickl, R., McDonnell, A., & Liston, A. (2014) · Applications in Plant Sciences · doi:10.3732/apps.1400042 · Cited by 469

Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy

Schuettpelz, E., & Pryer, K. M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811136106 · Cited by 462

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

Wiens, J. J., & Morrill, M. C. (2011) · Systematic Biology · doi:10.1093/sysbio/syr025 · Cited by 461

Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species

Muñoz, J. F., Gade, L., Chow, N. A., Loparev, V. N., Juieng, P., Berkow, E. L., Farrer, R. A., Litvintseva, A. P., & Cuomo, C. A. (2018) · Nature Communications · doi:10.1038/s41467-018-07779-6 · Cited by 458

Diverse uncultivated ultra-small bacterial cells in groundwater

Luef, B., Frischkorn, K. R., Wrighton, K. C., Holman, H. N., Birarda, G., Thomas, B. C., Singh, A., Williams, K. H., Siegerist, C. E., Tringe, S. G., et al. (2015) · Nature Communications · doi:10.1038/ncomms7372 · Cited by 457

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella

Rice, D. W., Alverson, A. J., Richardson, A. O., Young, G. J., Sanchez-Puerta, M. V., Munzinger, J., Barry, K., Boore, J. L., Zhang, Y., dePamphilis, C. W., et al. (2013) · Science · doi:10.1126/science.1246275 · Cited by 456

Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting

Gostic, K. M., Ambrose, M. R., Worobey, M., & Lloyd‐Smith, J. O. (2016) · Science · doi:10.1126/science.aag1322 · Cited by 456

Genome‐wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the L ake V ictoria cichlid adaptive radiation

Wagner, C. E., Keller, I., Wittwer, S., Selz, O. M., Mwaiko, S., Greuter, L., Sivasundar, A., & D, O. S. C. (2012) · Molecular Ecology · doi:10.1111/mec.12023 · Cited by 452

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Schwager, E. E., Sharma, P. P., Clarke, T. H., Leite, D. J., Wierschin, T., Pechmann, M., Akiyama‐Oda, Y., Esposito, L. A., Bechsgaard, J., Bilde, T., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0399-x · Cited by 451

Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish

Goldstone, J. V., McArthur, A. G., Kubota, A., Zanette, J., Parente, T. E., Jönsson, M. E., Nelson, D. R., & Stegeman, J. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-643 · Cited by 449

Genomic Outposts Serve the Phylogenomic Pioneers: Designing Novel Nuclear Markers for Genomic DNA Extractions of Lepidoptera

Wahlberg, N., & Wheat, C. W. (2008) · Systematic Biology · doi:10.1080/10635150802033006 · Cited by 449

Ionotropic Receptors (IRs): Chemosensory ionotropic glutamate receptors in Drosophila and beyond

Rytz, R., Croset, V., & Benton, R. (2013) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2013.02.007 · Cited by 448

The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life.

Atkinson, G. C., Tenson, T., & Hauryliuk, V. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023479 · Cited by 447

Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation

Xue, J., Zhou, X. Y., Zhang, C., Yu, L., Fan, H., Wang, Z., Xu, H., Xi, Y., Zhou, W., Zhou, W.-W., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0521-0 · Cited by 446

Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses

Yarza, P., Ludwig, W., Euzéby, J. P., Amann, R., SCHLEIFER, K. H., Glöckner, F. O., & Rossello-Mora, R. A. (2010) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2010.08.001 · Cited by 444

Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species–rich clades

The Legume Phylogeny Working Group, Bruneau, A., Doyle, J. J., Herendeen, P. S., Hughes, C. E., Kenicer, G., Lewis, G. P., Mackinder, B. A., Pennington, R. T., Sanderson, M. J., et al. (2013) · Taxon · doi:10.12705/622.8 · Cited by 443

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Goff, S. A., Vaughn, M. W., McKay, S., Lyons, E. H., Stapleton, A. E., Gessler, D. D. G., Matasci, N., Wang, L., Hanlon, M. R., Lenards, A., et al. (2011) · Frontiers in Plant Science · doi:10.3389/fpls.2011.00034 · Cited by 443

Acoelomorph flatworms are deuterostomes related to Xenoturbella

Philippe, H., Brinkmann, H., Copley, R. R., Moroz, L. L., Nakano, H., Poustka, A. J., Wållberg, A., Peterson, K. J., & Telford, M. J. (2011) · Nature · doi:10.1038/nature09676 · Cited by 441

Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

Baltrus, D. A., Nishimura, M. T., Romanchuk, A., Chang, J. H., Mukhtar, M. S., Cherkis, K., Roach, J. M., Grant, S. R., Jones, C. D., & Dangl, J. L. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002132 · Cited by 442

The water lily genome and the early evolution of flowering plants

Zhang, L., Chen, F., Zhang, X., Li, Z., Zhao, Y., Lohaus, R., Chang, X., Dong, W., Ho, S. Y. W., Liu, X., et al. (2019) · Nature · doi:10.1038/s41586-019-1852-5 · Cited by 438

Evolutionary origin of insect– Wolbachia nutritional mutualism

Nikoh, N., Hosokawa, T., Moriyama, M., Oshima, K., Hattori, M., & Fukatsu, T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1409284111 · Cited by 435

Adaptive Evolution within Gut Microbiomes of Healthy People

Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.007 · Cited by 434

Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus

Kikuchi, T., Cotton, J. A., Dalzell, J. J., Hasegawa, K., Kanzaki, N., McVeigh, P., Takanashi, T., Tsai, I. J., Assefa, S., Cock, P., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002219 · Cited by 434

Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts

Webster, N. S., Taylor, M. W., Behnam, F., Lücker, S., Rattei, T., Whalan, S., Horn, M., & Wagner, M. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02065.x · Cited by 434

Thirteen Camelliachloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

Huang, H., Shi, C., Liu, Y., Mao, S., & Gao, L.-Z. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-151 · Cited by 433

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

Zeng, L., Zhang, Q., Sun, R., Kong, H., Zhang, N., & Mā, H. (2014) · Nature Communications · doi:10.1038/ncomms5956 · Cited by 430

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Yoshida, K., Schuenemann, V. J., Cano, L. M., Pais, M., Mishra, B., Sharma, R., Lanz, C., Martin, F. N., Kamoun, S., Krause, J., et al. (2013) · eLife · doi:10.7554/elife.00731 · Cited by 430

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

Altenhoff, A., & Dessimoz, C. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000262 · Cited by 429

Resolving the evolutionary relationships of molluscs with phylogenomic tools

Smith, S. A., Wilson, N. G., Goetz, F., Feehery, C., Andrade, S. C. S., Rouse, G. W., Giribet, G., & Dunn, C. W. (2011) · Nature · doi:10.1038/nature10526 · Cited by 429

Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker

Allio, R., Donegà, S., Galtier, N., & Nabholz, B. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx197 · Cited by 428

Inferring Phylogenies with RAxML-VI-HPC

Stamatakis, A. (2006)

COMPUTING LARGE PHYLOGENIES WITH STATISTICAL METHODS: PROBLEMS & SOLUTIONS

P, S. A., Ludwig, T., Meier, H., & Department Of Computer Science (2015)

RAxML: A Parallel Program for Phylogenetic Tree Inference

Stamatakis, A. P., Stamatakis, R. P., Meier, H., & Ludwig, T. (2003)

A fast program for maximum likelihood-based inference of large phylogenetic trees

Stamatakis, A., Ludwig, T. G., & Meier, H. (2004) · ACM Symposium on Applied Computing · doi:10.1145/967900.967940 · Cited by 28

Parallel Inference of a 10.000-Taxon Phylogeny with Maximum Likelihood

Stamatakis, A., Ludwig, T. G., & Meier, H. (2004) · Lecture notes in computer science · doi:10.1007/978-3-540-27866-5_134 · Cited by 23