MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

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Jalview Version 2—a multiple sequence alignment editor and analysis workbench

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HMMER web server: interactive sequence similarity searching

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A Statistical Method for Evaluating Systematic Relationships

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Atlas of protein sequence and structure

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CLUSTAL: a package for performing multiple sequence alignment on a microcomputer

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Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

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Clustering of highly homologous sequences to reduce the size of large protein databases

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aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity

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Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era

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A beginner's guide to eukaryotic genome annotation

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Protein structure prediction from sequence variation

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phyloXML: XML for evolutionary biology and comparative genomics

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A strategy for the rapid multiple alignment of protein sequences

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PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

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Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

Yamada, K. D., Tomii, K., & Katoh, K. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw412 · Cited by 351 · see citing works

The alignment of sets of sequences and the construction of phyletic trees: An integrated method

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Adding unaligned sequences into an existing alignment using MAFFT and LAST

Katoh, K., & Frith, M. C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts578 · Cited by 242 · see citing works

COFFEE: an objective function for multiple sequence alignments.

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Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web

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Aligning short reads to reference alignments and trees

Berger, S., & Stamatakis, A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr320 · Cited by 191 · see citing works

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

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Ultra-large alignments using phylogeny-aware profiles

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Optimal alignment between groups of sequences and its application to multiple sequence alignment

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Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

Löytynoja, A., Vilella, A. J., & Goldman, N. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts198 · Cited by 123 · see citing works

Sequence embedding for fast construction of guide trees for multiple sequence alignment

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MaxAlign: maximizing usable data in an alignment

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PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences

Katoh, K., & Toh, H. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl592 · Cited by 106 · see citing works

A novel randomized iterative strategy for aligning multiple protein sequences

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Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment

Gotoh, O., Morita, M., & Nelson, D. R. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-189 · Cited by 61 · see citing works

F AST SP: linear time calculation of alignment accuracy

Mirarab, S., & Warnow, T. J. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr553 · Cited by 61 · see citing works

Making automated multiple alignments of very large numbers of protein sequences

Sievers, F., Dineen, D. G., Wilm, A., & Higgins, D. G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt093 · Cited by 55 · see citing works

Simple chained guide trees give high-quality protein multiple sequence alignments

Boyce, K., Sievers, F., & Higgins, D. G. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405628111 · Cited by 40 · see citing works

Protein multiple sequence alignment benchmarking through secondary structure prediction

Le, Q., Sievers, F., & Higgins, D. G. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btw840 · Cited by 35 · see citing works

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Tan, G., Gil, M., Löytynoja, A., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1417526112 · Cited by 24 · see citing works

MisPred: a resource for identification of erroneous protein sequences in public databases

Nagy, A., & Patthy, L. (2013) · Database · doi:10.1093/database/bat053 · Cited by 18 · see citing works

Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments

Fox, G., Sievers, F., & Higgins, D. G. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv592 · Cited by 18 · see citing works

Systematic exploration of guide-tree topology effects for small protein alignments

Sievers, F., Hughes, G. M., & Higgins, D. G. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-338 · Cited by 12 · see citing works

BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans

Sahin, U., Muik, A., Vogler, I., Derhovanessian, E., Kranz, L. M., Vormehr, M., Quandt, J., Bidmon, N., Ulges, A., Baum, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03653-6 · Cited by 845 · see citing works

Predicting multiple conformations via sequence clustering and AlphaFold2

Wayment-Steele, H. K., Ojoawo, A., Otten, R., Apitz, J. M., Pitsawong, W., Hömberger, M., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Nature · doi:10.1038/s41586-023-06832-9 · Cited by 545 · see citing works

Computed structures of core eukaryotic protein complexes

Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S. R., et al. (2021) · Science · doi:10.1126/science.abm4805 · Cited by 542 · see citing works

Detailed characterization of the Arthrospira type species separating commercially grown taxa into the new genus Limnospira (Cyanobacteria)

Nowicka-Krawczyk, P., Mühlsteinová, R., & Hauer, T. (2019) · Scientific Reports · doi:10.1038/s41598-018-36831-0 · Cited by 185 · see citing works

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance

Kamrad, S., Grossbach, J., Rodríguez‐López, M., Mülleder, M., Townsend, S., Cappelletti, V., Stojanovski, G., Correia‐Melo, C., Picotti, P., Beyer, A., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199270 · Cited by 40 · see citing works

Monospecific renaming within the cyanobacterial genus <i>Limnospira</i> (Spirulina) and consequences for food authorization

Roussel, T., Halary, S., Duval, C., Piquet, B., Cadoret, J.-P., Vernès, L., Bernard, C., & Marie, B. (2023) · Journal of Applied Microbiology · doi:10.1093/jambio/lxad159 · Cited by 39 · see citing works

High-quality whole-genome sequence analysis of Lactobacillus paragasseri UBLG-36 reveals oxalate-degrading potential of the strain

Mehra, Y., & Viswanathan, P. (2021) · PLOS ONE · doi:10.1371/journal.pone.0260116 · Cited by 27 · see citing works

The RIX domain defines a class of polymorphic T6SS effectors and secreted adaptors

Kanarek, K., Fridman, C. M., Bosis, E., & Salomon, D. (2023) · Nature Communications · doi:10.1038/s41467-023-40659-2 · Cited by 27 · see citing works

Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis in Bacillus subtilis to Provide Cytoprotection Against Sustained Osmotic Stress

Warmbold, B., Ronzheimer, S., Freibert, S.-A., Seubert, A., Hoffmann, T., & Bremer, E. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01700 · Cited by 17 · see citing works

Dirofilaria spp. infection in cats from the Mediterranean basin: diagnosis and epidemiology

Carbonara, M., Perles, L., Venco, L., Gabrielli, S., Barrs, V. R., Miró, G., Papadopoulos, E., Lima, C., Bouhsira, E., Baneth, G., et al. (2025) · International Journal for Parasitology · doi:10.1016/j.ijpara.2025.01.011 · Cited by 12 · see citing works

Cryo-EM structure of native honey bee vitellogenin

Montserrat-Canals, M., Schnelle, K., Leipart, V., Halskau, Ø., Amdam, G. V., Moeller, A., Cunha, E. S., & Luecke, H. (2025) · Nature Communications · doi:10.1038/s41467-025-58575-y · Cited by 7 · see citing works

A unique inhibitor conformation selectively targets the DNA polymerase PolC of Gram-positive priority pathogens

Urem, M., Friggen, A. H., Musch, N., Silverman, M. H., Swain, C. J., Barbachyn, M. R., Mortin, L. I., Yu, X., DeLuccia, R. J., Lamers, M. H., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65324-8 · Cited by 2 · see citing works

Alignment of protein sequences by their profiles

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Homology-extended sequence alignment

Simossis, V. A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki233 · Cited by 116 · see citing works

Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems

Grasso, C. S., & Lee, C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth126 · Cited by 121 · see citing works

Multiple Sequence Alignment

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INTERALIGN: interactive alignment editor for distantly related protein sequences

Pible, O., Imbert, G., & Pellequer, J. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti474 · Cited by 10 · see citing works