BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

BLAST+: architecture and applications

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QUAST: quality assessment tool for genome assemblies

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Accelerated Profile HMM Searches

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The COG database: an updated version includes eukaryotes

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CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

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Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences

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A novel hybrid gene prediction method employing protein multiple sequence alignments

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REAPR: a universal tool for genome assembly evaluation

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Assessing the gene space in draft genomes

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OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

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Accurate and universal delineation of prokaryotic species

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OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

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ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

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Exploring genome characteristics and sequence quality without a reference

Simpson, J. T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu023 · Cited by 141 · see citing works

Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi

Waterhouse, R. M., Zdobnov, E. M., & Kriventseva, E. V. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq083 · Cited by 87 · see citing works

A maturing understanding of the composition of the insect gene repertoire

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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021) · Nature Methods · doi:10.1038/s41592-020-01056-5 · Cited by 5,859 · see citing works

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02134-9 · Cited by 3,643 · see citing works

BUSCO applications from quality assessments to gene prediction and phylogenomics

Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx319 · Cited by 2,214 · see citing works

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

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A chromosome conformation capture ordered sequence of the barley genome

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MetaQUAST: evaluation of metagenome assemblies

Mikheenko, A., Saveliev, V., & Gurevich, A. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btv697 · Cited by 711 · see citing works

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0503-6 · Cited by 567 · see citing works

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

Narunsky-Haziza, L., Sepich-Poore, G. D., Livyatan, I., Asraf, O., Martino, C., Nejman, D., Gavert, N., Stajich, J. E., Amit, G., González, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.005 · Cited by 538 · see citing works

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 · see citing works

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., et al. (2019) · Science · doi:10.1126/science.aav6202 · Cited by 441 · see citing works

Ancient gene linkages support ctenophores as sister to other animals

Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362 · see citing works

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303 · see citing works

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Monat, C., Padmarasu, S., Lux, T., Wicker, T., Gundlach, H., Himmelbach, A., Ens, J., Li, C., Muehlbauer, G. J., Schulman, A. H., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1899-5 · Cited by 251 · see citing works

Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Musser, J. M., Schippers, K. J., Nickel, M., Mizzon, G., Kohn, A. B., Pape, C., Ronchi, P., Papadopoulos, N., Tarashansky, A. J., Hammel, J. U., et al. (2021) · Science · doi:10.1126/science.abj2949 · Cited by 242 · see citing works

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

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

Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants

Harris, B. J., Clark, J. W., Schrempf, D., Szöllősi, G. J., Donoghue, P. C. J., Hetherington, A. M., & Williams, T. A. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01885-x · Cited by 187 · see citing works

Dynamic pigmentary and structural coloration within cephalopod chromatophore organs

Williams, T. L., Senft, S. L., Yeo, J., Martín-Martínez, F. J., Kuzirian, A. M., Martin, C. A., DiBona, C. W., Chen, C.-T., Dinneen, S. R., Nguyen, H. T., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08891-x · Cited by 178 · see citing works

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic islands

Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000436 · Cited by 152 · see citing works

Non-photosynthetic predators are sister to red algae

Gawryluk, R. M. R., Tikhonenkov, D. V., Hehenberger, E., Husnik, F., Mylnikov, A. P., & Keeling, P. J. (2019) · Nature · doi:10.1038/s41586-019-1398-6 · Cited by 148 · see citing works

Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish

Powell, D. L., García-Olazábal, M., Keegan, M., Reilly, P., Du, K., Díaz-Loyo, A. P., Banerjee, S., Blakkan, D., Reich, D., Andolfatto, P., et al. (2020) · Science · doi:10.1126/science.aba5216 · Cited by 124 · see citing works

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

Laumer, C. E., Gruber-Vodicka, H., Hadfield, M. G., Pearse, V. B., Riesgo, A., Marioni, J. C., & Giribet, G. (2018) · eLife · doi:10.7554/elife.36278 · Cited by 112 · see citing works

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

Johnson, L. K., Alexander, H., & Brown, C. T. (2019) · GigaScience · doi:10.1093/gigascience/giy158 · Cited by 94 · see citing works

Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk

Kono, N., Nakamura, H., Mori, M., Yoshida, Y., Ohtoshi, R., Malay, A. D., Pedrazzoli Moran, D. A., Tomita, M., Numata, K., & Arakawa, K. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2107065118 · Cited by 99 · see citing works

A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise

Schreiber, M., Mascher, M., Wright, J., Padmarasu, S., Himmelbach, A., Heavens, D., Milne, L., Clavijo, B. J., Stein, N., & Waugh, R. (2020) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.119.401010 · Cited by 94 · see citing works

Genome-Wide Signatures of Adaptation to Extreme Environments in Red Algae

Cho, C. H., Park, S. I., Huang, T.-Y., Lee, Y., Ciniglia, C., Yadavalli, H. C., Yang, S. W., Bhattacharya, D., & Yoon, H. S. (2023) · Nature Communications · doi:10.1038/s41467-022-35566-x · Cited by 83 · see citing works

Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet

Hu, R., Li, X., Hu, Y., Zhang, R., Lv, Q., Zhang, M., Sheng, X., Zhao, F., Chen, Z., Ding, Y., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.003 · Cited by 55 · see citing works

The monoaminergic system is a bilaterian innovation

Goulty, M., Botton-Amiot, G., Rosato, E., Sprecher, S. G., & Feuda, R. (2023) · Nature Communications · doi:10.1038/s41467-023-39030-2 · Cited by 60 · see citing works

The complete telomere-to-telomere sequence of a mouse genome

Liu, J., Li, Q., Hu, Y., Yu, Y., Zheng, K., Li, D., Qin, L., & Yu, X. (2024) · Science · doi:10.1126/science.adq8191 · Cited by 57 · see citing works

Functional Strain Redundancy and Persistent Phage Infection in Swiss Hard Cheese Starter Cultures

Somerville, V., Berthoud, H., Schmidt, R. S., Bachmann, H.-P., Meng, Y. H., Fuchsmann, P., von Ah, U., & Engel, P. (2022) · The ISME Journal · doi:10.1038/s41396-021-01071-0 · Cited by 55 · see citing works

Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence

Fukushima, K., & Pollock, D. D. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01932-7 · Cited by 55 · see citing works

Structural Variation and Introgression from Wild Populations in East Asian Cattle Genomes Confer Adaptation to Local Environment

Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03052-2 · Cited by 53 · see citing works

Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids

Cenci, U., Sibbald, S. J., Curtis, B. A., Kamikawa, R., Eme, L., Moog, D., Henrissat, B., Maréchal, E., Chabi, M., Djemiel, C., et al. (2018) · BMC Biology · doi:10.1186/s12915-018-0593-5 · Cited by 53 · see citing works

Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca

Suzuki, S., Endoh, R., Manabe, R.-I., Ohkuma, M., & Hirakawa, Y. (2018) · Scientific Reports · doi:10.1038/s41598-017-18378-8 · Cited by 53 · see citing works

A chromosome-scale genome assembly and karyotype of the ctenophore <i>Hormiphora californensis</i>

Schultz, D. T., Francis, W. R., McBroome, J. D., Christianson, L. M., Haddock, S. H. D., & Green, R. E. (2021) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkab302 · Cited by 35 · see citing works

Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton

Alexander, H., Hu, S. K., Krinos, A. I., Pachiadaki, M., Tully, B. J., Neely, C. J., & Reiter, T. (2021) · doi:10.1101/2021.07.25.453713 · Cited by 67 · see citing works

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies

Matteoli, F. P., Passarelli-Araujo, H., Pedrosa-Silva, F., Olivares, F. L., & Venancio, T. M. (2020) · Genomics · doi:10.1016/j.ygeno.2019.07.003 · Cited by 27 · see citing works

Hybrid genome assembly and annotation of Danionella translucida

Kadobianskyi, M., Schulze, L., Schuelke, M., & Judkewitz, B. (2019) · Scientific Data · doi:10.1038/s41597-019-0161-z · Cited by 36 · see citing works

The vast majority of somatic mutations in plants are layer-specific

Goel, M., Campoy, J. A., Krause, K., Baus, L. C., Sahu, A., Sun, H., Walkemeier, B., Marek, M., Beaudry, R., Ruiz, D., et al. (2024) · Genome Biology · doi:10.1186/s13059-024-03337-0 · Cited by 31 · see citing works

Highly replicated evolution of parapatric ecotypes

James, M. E., Arenas-Castro, H., Groh, J. S., Allen, S. L., Engelstädter, J., & Ortiz-Barrientos, D. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab207 · Cited by 30 · see citing works

PSAURON: a tool for assessing protein annotation across a broad range of species

Sommer, M. J., Zimin, A. V., & Salzberg, S. L. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae189 · Cited by 29 · see citing works

Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project

Van Vlierberghe, M., Di Franco, A., Philippe, H., & Baurain, D. (2021) · BMC Research Notes · doi:10.1186/s13104-021-05717-2 · Cited by 27 · see citing works

Transcriptome dynamics and hub genes of green alga Nannochloris sp. JB17 under NaHCO3 stress

Wang, M., Ye, X., Wang, Y., Su, D., Liu, S., & Bu, Y. (2021) · Algal Research · doi:10.1016/j.algal.2021.102185 · Cited by 17 · see citing works

Speciation with gene flow between two Neotropical sympatric species (<i>Pitcairnia</i> spp.: Bromeliaceae)

Tavares, M. M., Ferro, M., Leal, B. S. S., & Palma‐Silva, C. (2022) · Ecology and Evolution · doi:10.1002/ece3.8834 · Cited by 15 · see citing works

Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle

Xia, X., Wang, F., Luo, X., Li, S., Lyu, Y., Zheng, Y., Ma, Z., Qu, K., Song, R., Liu, J., et al. (2025) · Advanced Science · doi:10.1002/advs.202503258 · Cited by 14 · see citing works

Convergent molecular evolution of thermogenesis and circadian rhythm in Arctic ruminants

Li, M., Li, X., Wu, Z., Zhang, G., Wang, N., Dou, M., Liu, S., Yang, C., Meng, G., Sun, H., et al. (2023) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2023.0538 · Cited by 12 · see citing works

Phylogenomics of a Saccharomyces cerevisiae cocoa strain reveals adaptation to a West African fermented food population

Díaz-Muñoz, C., Verce, M., De Vuyst, L., & Weckx, S. (2022) · iScience · doi:10.1016/j.isci.2022.105309 · Cited by 10 · see citing works

Genomes of critically endangered saola are shaped by population structure and purging

Garcia-Erill, G., Liu, S., Le, M. D., Hurley, M. M., Nguyen, H. D., Nguyen, D. Q., Nguyen, D. H., Santander, C. G., Sánchez Barreiro, F., Gomes Martins, N. F., et al. (2025) · Cell · doi:10.1016/j.cell.2025.03.040 · Cited by 10 · see citing works

Chromosomal-level reference genome assembly of the North American wolverine (<i>Gulo gulo luscus</i>): a resource for conservation genomics

Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Wintle, R. F., Engstrom, M. D., Stacy, E., Waits, L. P., Scrafford, M., & Scherer, S. W. (2022) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkac138 · Cited by 6 · see citing works

Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics

Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Paton, T., Wintle, R. F., Engstrom, M. D., Gunn, A., & Scherer, S. W. (2024) · Scientific Reports · doi:10.1038/s41598-024-67270-9 · Cited by 4 · see citing works

Chromosome-level genome assembly of the glass catfish (&lt;i&gt;Kryptopterus vitreolus&lt;/i&gt;) reveals molecular clues to its transparent phenotype

Bian, C., 深圳大学生命与海洋科学学院水产基因组学实验室, 广. 深. 5., Laboratory of Aquatic Genomics, C. O. L. S. A. O., Li, R.-H., Ruan, Z.-Q., Chen, W.-T., Huang, Y., Liu, L.-Y., Zhou, H.-L., Chong, C.-M., et al. (2024) · Zoological Research · doi:10.24272/j.issn.2095-8137.2023.396 · Cited by 4 · see citing works

Draft Genome Assembly of an Iconic Arctic Species: Muskox (Ovibos moschatus)

Prewer, E., Kutz, S., Leclerc, L.-M., & Kyle, C. J. (2022) · Genes · doi:10.3390/genes13050809 · Cited by 3 · see citing works

The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway &amp; Rüber, 2009)

Rüber, L., Britz, R., Conway, K., Bista, I., McCarthy, S., Wood, J., Smith, M., Oliver, K., Howe, K., & Durbin, R. (2024) · Wellcome Open Research · doi:10.12688/wellcomeopenres.21117.1 · Cited by 3 · see citing works

Méthodes d'analyse comparée des pangénomes procaryotes : explorer la diversité génomique inter-espèces pour une meilleure compréhension du métabolisme

Arnoux, J. (2026) · Thèse de doctorat, Université Paris-Saclay / PPanGGOLiN · doi:10.70675/eee354d9zf63dz48ebz9444zd1809f8fb74d

EAnnot: A genome annotation tool using experimental evidencePreprint

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Hayai-Annotation Plants: an ultra-fast and comprehensive gene annotation system in plantsPreprint

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EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

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OligoRAP – an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity

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Towards multidimensional genome annotation

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