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Parallelization of the MAFFT multiple sequence alignment program

https://doi.org/10.1093/bioinformatics/btq224
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/prot.20527openalex-snapshot
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
inferredcites →https://doi.org/10.1006/jmbi.1996.0679openalex-snapshot
Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments
inferredcites →https://doi.org/10.1007/bf02603120openalex-snapshot
Progressive sequence alignment as a prerequisitetto correct phylogenetic trees
inferredcites →https://doi.org/10.1016/0022-2836(87)90316-0openalex-snapshot
A strategy for the rapid multiple alignment of protein sequences
inferredcites →https://doi.org/10.1093/bib/bbn013openalex-snapshot
Recent developments in the MAFFT multiple sequence alignment program
inferredcites →https://doi.org/10.1093/bioinformatics/11.1.13openalex-snapshot
Comprehensive study on iterative algorithms of multiple sequence alignment
inferredcites →https://doi.org/10.1093/bioinformatics/15.1.87openalex-snapshot
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.
inferredcites →https://doi.org/10.1093/bioinformatics/18.9.1270openalex-snapshot
Parallelized multiple alignment
inferredcites →https://doi.org/10.1093/bioinformatics/7.4.479openalex-snapshot
A novel randomized iterative strategy for aligning multiple protein sequences
inferredcites →https://doi.org/10.1093/bioinformatics/9.3.267openalex-snapshot
Multiple sequence alignment by parallel simulated annealing
inferredcites →https://doi.org/10.1093/bioinformatics/9.3.361openalex-snapshot
Optimal alignment between groups of sequences and its application to multiple sequence alignment
inferredcites →https://doi.org/10.1093/bioinformatics/9.4.397openalex-snapshot
Multiple alignment of sequences on parallel computers
inferredcites →https://doi.org/10.1093/bioinformatics/btg192openalex-snapshot
ClustalW-MPI: ClustalW analysis using distributed and parallel computing
inferredcites →https://doi.org/10.1093/bioinformatics/btg250openalex-snapshot
Parallel BLAST on split databases
inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
inferredcites →https://doi.org/10.1109/ipdps.2006.1639537openalex-snapshot
MT-ClustalW: multithreading multiple sequence alignment
inferredcites →https://doi.org/10.5555/1898699.1898764openalex-snapshot
MT-ClustalW: multithreading multiple sequence alignment

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Study of three Scenedesmaceae strains: morphology, molecular phylogeny, growth and carotenogenesis
inferred← citeshttps://doi.org/10.1007/s11557-012-0848-4openalex-snapshot
Species complexes in Hericium (Russulales, Agaricomycota) and a new species - Hericium rajchenbergii - from southern South America
inferred← citeshttps://doi.org/10.1007/s11557-012-0861-7openalex-snapshot
Morphological and phylogenetic characterisation of two new species of Phyllosticta from China
inferred← citeshttps://doi.org/10.1007/s11557-015-1096-1openalex-snapshot
Cytospora from Ulmus pumila in Northern China
inferred← citeshttps://doi.org/10.1007/s11557-015-1104-5openalex-snapshot
Diaporthe rostrata, a novel ascomycete from Juglans mandshurica associated with walnut dieback
inferred← citeshttps://doi.org/10.1007/s11557-017-1348-3openalex-snapshot
An ultrastructural study of spore wall development and septal pores in species of the Pachyphlodes (Pezizaceae, Pezizales) lineage, with a description of the new species Pachyphlodes annagardnerae
inferred← citeshttps://doi.org/10.1007/s11557-018-1395-4openalex-snapshot
Diaporthe from walnut tree (Juglans regia) in China, with insight of the Diaporthe eres complex
inferred← citeshttps://doi.org/10.1007/s11557-020-01606-3openalex-snapshot
Proposal for a subdivision of the family Psathyrellaceae based on a taxon-rich phylogenetic analysis with iterative multigene guide tree
inferred← citeshttps://doi.org/10.1007/s11557-021-01666-zopenalex-snapshot
Phylogeny of cercosporoid fungi (Mycosphaerellaceae, Mycosphaerellales) from Hawaii and New York reveals novel species within the Cercospora beticola complex
inferred← citeshttps://doi.org/10.1007/s11557-021-01739-zopenalex-snapshot
Phylogenetic analysis of Engleromyces sinensis and identification of cytochalasin D from culture
inferred← citeshttps://doi.org/10.1007/s11692-015-9356-1openalex-snapshot
Rising the Persian Gulf Black-Lip Pearl Oyster to the Species Level: Fragmented Habitat and Chaotic Genetic Patchiness in Pinctada persica
inferred← citeshttps://doi.org/10.1007/s11802-022-5056-5openalex-snapshot
Complete Mitochondrial Genome Analysis of Daphniopsis tibetana (Branchiopoda: Diplostraca): New Insights into the Taxonomy of the Genus and Its Phylogenetic Implications for Branchiopoda
inferred← citeshttps://doi.org/10.1007/s12038-023-00357-zopenalex-snapshot
Characterization of complete mitochondrial genomes of five noctuoid moths (Lepidoptera: Noctuoidea) and their phylogenetic implications
inferred← citeshttps://doi.org/10.1007/s12298-026-01795-3openalex-snapshot
Biochemical characteristics and antioxidant potential of Vischeria magna
inferred← citeshttps://doi.org/10.1007/s12539-013-0137-1openalex-snapshot
Evolution driven structural changes in CENP-E motor domain
inferred← citeshttps://doi.org/10.1007/s13205-023-03640-wopenalex-snapshot
Prevalence of Deltaproteobacterial sequences in nifH gene pools associated with the rhizosphere of native switchgrass from Tall Grass Prairie (Oklahoma, USA)
inferred← citeshttps://doi.org/10.1007/s13225-012-0166-9openalex-snapshot
Phylogenetic placement of lichenicolous Phoma species in the Phaeosphaeriaceae (Pleosporales, Dothideomycetes)
inferred← citeshttps://doi.org/10.1007/s13225-013-0249-2openalex-snapshot
Species of the Colletotrichum gloeosporioides complex associated with anthracnose diseases of Proteaceae
inferred← citeshttps://doi.org/10.1007/s13225-013-0277-yopenalex-snapshot
Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies
inferred← citeshttps://doi.org/10.1007/s13225-017-0380-6openalex-snapshot
High levels of endemism among Galapagos basidiolichens
inferred← citeshttps://doi.org/10.1007/s13225-020-00445-7openalex-snapshot
Reallocation of foliicolous species of the genus Strigula into six genera (lichenized Ascomycota, Dothideomycetes, Strigulaceae)
inferred← citeshttps://doi.org/10.1007/s13225-020-00453-7openalex-snapshot
Culturable mycobiota from Karst caves in China II, with descriptions of 33 new species
inferred← citeshttps://doi.org/10.1007/s13225-024-00538-7openalex-snapshot
A re-evaluation of Diaporthe: refining the boundaries of species and species complexes
inferred← citeshttps://doi.org/10.1007/s13313-012-0163-1openalex-snapshot
Lasiodiplodia species associated with dieback disease of mango (Mangifera indica) in Egypt
inferred← citeshttps://doi.org/10.1007/s13313-012-0188-5openalex-snapshot
Ilyonectria black foot rot associated with Proteaceae
inferred← citeshttps://doi.org/10.1007/s13314-015-0170-5openalex-snapshot
Lasiodiplodia pseudotheobromae causes pedicel and peduncle discolouration of grapes in China
inferred← citeshttps://doi.org/10.1007/s13337-014-0246-4openalex-snapshot
First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash
inferred← citeshttps://doi.org/10.1007/s13353-016-0357-2openalex-snapshot
Genome-wide identification, characterisation and expression profiles of calcium-dependent protein kinase genes in barley (Hordeum vulgare L.)
inferred← citeshttps://doi.org/10.1007/s13355-016-0409-4openalex-snapshot
Sexually biased expression of odorant-binding proteins and chemosensory proteins in Asian corn borer Ostrinia furnacalis (Lepidoptera: Crambidae)
inferred← citeshttps://doi.org/10.1007/s13762-023-04766-3openalex-snapshot
Toxic effect of copper on soil microalgae: experimental data and critical review
inferred← citeshttps://doi.org/10.1007/s40415-023-00973-xopenalex-snapshot
Plastome comparison reveals hotspots of nucleotide diversity and positive selection pressure on accD, matK, psaA and rbcL genes in Smilacaceae
inferred← citeshttps://doi.org/10.1007/s40415-025-01090-7openalex-snapshot
On the ecological value of the pseudopetiole in Cyperaceae and its usefulness in Liliopsida
inferred← citeshttps://doi.org/10.1007/s42770-025-01858-9openalex-snapshot
Terrestrial bacterial isolate capability of producing surface-active biosurfactant: genetic identification, biochemical and morphological approach
inferred← citeshttps://doi.org/10.1016/b978-1-78548-216-8.50014-2openalex-snapshot
Bibliography
inferred← citeshttps://doi.org/10.1016/j.algal.2018.06.008openalex-snapshot
Description of a new species of soil algae, Parietochloris grandis sp. nov., and study of its fatty acid profiles under different culturing conditions
inferred← citeshttps://doi.org/10.1016/j.aquatox.2011.12.010openalex-snapshot
Functional characterization of four metallothionein genes in Daphnia pulex exposed to environmental stressors
inferred← citeshttps://doi.org/10.1016/j.aquatox.2019.01.002openalex-snapshot
The retinoic acid receptor (RAR) in molluscs: Function, evolution and endocrine disruption insights
inferred← citeshttps://doi.org/10.1016/j.archoralbio.2012.10.017openalex-snapshot
Identification of disulphide stress–responsive extracytoplasmic function sigma factors in Rothia mucilaginosa
inferred← citeshttps://doi.org/10.1016/j.bbabio.2011.08.006openalex-snapshot
Structural elements of the mitochondrial preprotein-conducting channel Tom40 dissolved by bioinformatics and mass spectrometry
inferred← citeshttps://doi.org/10.1016/j.bbagen.2016.11.007openalex-snapshot
The effect of single nucleotide polymorphisms in G-rich regions of high-risk human papillomaviruses on structural diversity of DNA
inferred← citeshttps://doi.org/10.1016/j.bbamcr.2020.118822openalex-snapshot
From economy to luxury: Copper homeostasis in Chlamydomonas and other algae
inferred← citeshttps://doi.org/10.1016/j.bbrc.2012.11.044openalex-snapshot
Molecular approaches for structural characterization of a new potassium channel blocker from Tityus stigmurus venom: cDNA cloning, homology modeling, dynamic simulations and docking
inferred← citeshttps://doi.org/10.1016/j.biochi.2025.10.013openalex-snapshot
Functional and immunological variability of Viperid venoms across continents and cross-neutralization by Peruvian antivenoms
inferred← citeshttps://doi.org/10.1016/j.biopha.2022.113380openalex-snapshot
Farnesoid X receptor activation by the novel agonist TC-100 (3α, 7α, 11β-Trihydroxy-6α-ethyl-5β-cholan-24-oic Acid) preserves the intestinal barrier integrity and promotes intestinal microbial reshaping in a mouse model of obstructed bile acid flow
inferred← citeshttps://doi.org/10.1016/j.cbi.2012.11.009openalex-snapshot
Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs)
inferred← citeshttps://doi.org/10.1016/j.cbpa.2024.111694openalex-snapshot
Light sensitivity in Beroidae ctenophores: Insights from laboratory studies and genomics
inferred← citeshttps://doi.org/10.1016/j.chembiol.2018.11.001openalex-snapshot
(ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition
inferred← citeshttps://doi.org/10.1016/j.chemosphere.2017.05.064openalex-snapshot
Cloning and functional characterization of a retinoid X receptor orthologue in Platynereis dumerilii: An evolutionary and toxicological perspective
inferred← citeshttps://doi.org/10.1016/j.chom.2025.10.020openalex-snapshot
Hologenomic insights into the molecular adaptation of deep-sea coral Bathypathes pseudoalternata
inferred← citeshttps://doi.org/10.1016/j.cmi.2021.01.018openalex-snapshot
A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2012.12.009openalex-snapshot
A data parallel strategy for aligning multiple biological sequences on multi-core computers
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2014.02.006openalex-snapshot
Risk classification of cancer survival using ANN with gene expression data from multiple laboratories
inferred← citeshttps://doi.org/10.1016/j.cub.2015.06.023openalex-snapshot
Discovery of an Unconventional Centromere in Budding Yeast Redefines Evolution of Point Centromeres
inferred← citeshttps://doi.org/10.1016/j.cub.2018.08.018openalex-snapshot
Unicellular Origin of the Animal MicroRNA Machinery
inferred← citeshttps://doi.org/10.1016/j.cub.2019.09.074openalex-snapshot
Intracellular Infection of Diverse Diatoms by an Evolutionary Distinct Relative of the Fungi
inferred← citeshttps://doi.org/10.1016/j.cub.2023.12.021openalex-snapshot
Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response
inferred← citeshttps://doi.org/10.1016/j.dib.2016.05.055openalex-snapshot
Molecular, morphological and fossil input data for inferring relationship among viviparous brotulas (Bythitidae) – Resulting in a family status change for Dinematichthyidae
inferred← citeshttps://doi.org/10.1016/j.dib.2016.06.043openalex-snapshot
Input data for inferring species distributions in Kyphosidae world-wide
inferred← citeshttps://doi.org/10.1016/j.dsr.2020.103396openalex-snapshot
Metagenomic studies of SAR202 bacteria at the full-ocean depth in the Mariana Trench
inferred← citeshttps://doi.org/10.1016/j.dsr.2022.103873openalex-snapshot
Isolation and characterization of piezotolerant fungi from Mariana Trench sediment
inferred← citeshttps://doi.org/10.1016/j.ejop.2022.125943openalex-snapshot
Morphological and molecular reinvestigation of acanthoecid species III. – Kalathoeca cupula (Leadbeater, 1972) gen. et comb. nov. (=Stephanoeca cupula (Leadbeater) Thomsen, 1988)
inferred← citeshttps://doi.org/10.1016/j.fm.2024.104615openalex-snapshot
Characterization of core microbiota of barley seeds from different continents for origin tracing and quarantine pathogen assessment
inferred← citeshttps://doi.org/10.1016/j.foodres.2022.111998openalex-snapshot
Applying meta-data of soybean grain in origin trace and quarantine inspection
inferred← citeshttps://doi.org/10.1016/j.funbio.2014.06.006openalex-snapshot
Diaporthe species occurring on Lithocarpus glabra in China, with descriptions of five new species
inferred← citeshttps://doi.org/10.1016/j.funbio.2014.11.003openalex-snapshot
Morphological and molecular characterisation of Diaporthe species associated with grapevine trunk disease in China
inferred← citeshttps://doi.org/10.1016/j.funbio.2015.06.010openalex-snapshot
Five new species of entomopathogenic fungi from the Amazon and evolution of neotropical Ophiocordyceps
inferred← citeshttps://doi.org/10.1016/j.funbio.2015.08.003openalex-snapshot
Morphological and molecular characterisation of Geosmithia species on European elms
inferred← citeshttps://doi.org/10.1016/j.funbio.2016.05.005openalex-snapshot
Molecular phylogeny and taxonomy of Lagenidium -like oomycetes pathogenic to mammals
inferred← citeshttps://doi.org/10.1016/j.funbio.2016.12.004openalex-snapshot
A molecular and morphological re-examination of the generic limits of truffles in the tarzetta-geopyxis lineage – Densocarpa, Hydnocystis, and Paurocotylis
inferred← citeshttps://doi.org/10.1016/j.funeco.2014.02.005openalex-snapshot
Cultivated and fallow fields harbor distinct communities of Basidiomycota
inferred← citeshttps://doi.org/10.1016/j.funeco.2015.10.004openalex-snapshot
Colonization of new land by arbuscular mycorrhizal fungi
inferred← citeshttps://doi.org/10.1016/j.future.2012.12.019openalex-snapshot
Performance evaluation of parallel strategies in public clouds: A study with phylogenomic workflows
inferred← citeshttps://doi.org/10.1016/j.future.2014.10.009openalex-snapshot
Optimizing virtual machine allocation for parallel scientific workflows in federated clouds
inferred← citeshttps://doi.org/10.1016/j.gecco.2022.e02214openalex-snapshot
Genetic patterns reveal differences between the invasion processes of common ragweed in urban and non-urban ecosystems
inferred← citeshttps://doi.org/10.1016/j.gene.2016.10.030openalex-snapshot
The genome of serotype VI Streptococcus agalactiae serotype VI and comparative analysis
inferred← citeshttps://doi.org/10.1016/j.gene.2017.10.009openalex-snapshot
Complete structure and variation of the chloroplast genome of Agropyron cristatum (L.) Gaertn
inferred← citeshttps://doi.org/10.1016/j.gene.2025.149324openalex-snapshot
Chloroplast-nuclear genome interaction drives asymmetric inverted repeats in chloroplast genome of Huperzia
inferred← citeshttps://doi.org/10.1016/j.heliyon.2024.e32807openalex-snapshot
The presence of plasmenyl ether lipids in Capsaspora owczarzaki suggests a premetazoan origin of plasmalogen biosynthesis in animals
inferred← citeshttps://doi.org/10.1016/j.ibmb.2017.01.006openalex-snapshot
Comparative analysis of the brain transcriptome in a hyper-aggressive fruit fly, Drosophila prolongata
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2020.08.151openalex-snapshot
Biochemical and molecular characterization of a restriction endonuclease Tvu2HI from Thermoactinomyces vulgaris 2H and study of its R-M system
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.133449openalex-snapshot
Evolutionary history and activity towards oligosaccharides and polysaccharides of GH3 glycosidases from an Antarctic marine bacterium
inferred← citeshttps://doi.org/10.1016/j.ijpara.2017.07.008openalex-snapshot
Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa)
inferred← citeshttps://doi.org/10.1016/j.ijppaw.2024.101020openalex-snapshot
A new genus and species of isosporoid coccidium from captive green tree frogs, Ranoidea caerulea (Anura: Hylidae)
inferred← citeshttps://doi.org/10.1016/j.isci.2023.107033openalex-snapshot
Early genome erosion and internal phage-symbiont-host interaction in the endosymbionts of a cold-seep tubeworm
inferred← citeshttps://doi.org/10.1016/j.jaridenv.2022.104921openalex-snapshot
Survey and identification of coinfecting Botryosphaeriales causing stem canker diseases of Eucalyptus camaldulensis in Ethiopia
inferred← citeshttps://doi.org/10.1016/j.jbc.2023.102981openalex-snapshot
Aim18p and Aim46p are chalcone isomerase domain–containing mitochondrial hemoproteins in Saccharomyces cerevisiae
inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107770openalex-snapshot
Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains
inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107838openalex-snapshot
Reversal of tyrosine-linked ADP-ribosylation by ARH3 and PARG
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