MUSCLE: multiple sequence alignment with improved accuracy and speed

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.

• Publication date

  2004-08-16

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.1109/CSB.2004.1332560
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Influence of cultivation temperature on the ligninolytic activity of selected fungal strains

  2006influential reference
• The alignment of sets of sequences and the construction of phyletic trees: An integrated method

  2005cited by this paper
• Align-m-a new algorithm for multiple alignment of highly divergent sequences

  2004cited by this paper
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.

  2004cited by this paper
• Local homology recognition and distance measures in linear time using compressed amino acid alphabets.

  2004cited by this paper
• Recent progresses in multiple sequence alignment : a survey

  2001cited by this paper
• BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations

  2001cited by this paper
• T-Coffee: A novel method for fast and accurate multiple sequence alignment.

  2000cited by this paper
• SMART: identification and annotation of domains from signalling and extracellular protein sequences

  1999cited by this paper
• Comprehensive study on iterative algorithms of multiple sequence alignment

  1995cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994cited by this paper
• The neutral theory of molecular evolution.

  1983cited by this paper
• Numerical Taxonomy

  1962cited by this paper

• Comprehensive Genomic Profiling and In Vitro Probiotic and Safety Assessments of Enterococcus faecium UFAS147 Isolated from Moroccan Goat Feces

  2025cites this paper
• Efficient Recovery of Phosphorus from Wastewater Using Calcium-Based Modified Biochar: Removal Performance, Adsorption Mechanism, and Resource Utilization

  2025cites this paper
• Epidemiological assessment and outbreak report of Trypanosoma vivax in dairy cattle from the Brazilian Semiarid region

  2025cites this paper
• Host–Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts

  2024cites this paper
• Genomic Insights Into Enterococcus mundtii 203: A Promising Probiotic Candidate Isolated From Camel Feces

  2024cites this paper
• Novel DNA methylation changes in mouse lungs associated with chronic smoking

  2024influential citation
• The Origin and Ecology of a Likely Introduced Population of Southern Black-Bellied Salamanders (Desmognathus amphileucus)

  2024influential citation
• The Identification, Characterization, and Functional Analysis of the Sugar Transporter Gene Family of the Rice False Smut Pathogen, Villosiclava virens

  2024cites this paper
• Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial

  2024cites this paper
• Freezing stress tolerance of benthic freshwater diatoms from the genus Pinnularia: Comparison of strains from polar, alpine, and temperate habitats

  2024cites this paper
• Unified Aedes aegypti Protein Resource Database (UAAPRD): An Integrated High-Throughput In Silico Platform for Comprehensive Protein Structure Modeling and Functional Target Analysis to Enhance Vector Control Strategies

  2024cites this paper
• Time‐calibrated phylogeny of Daphne (Thymelaeaceae): Pre‐mediterranean temporal origin of the sclerophyllous Daphne gnidium

  2023influential citation
• Response of Intestinal Microbiota of Tiger Puffer (Takifugu rubripes) to the Fish Oil Finishing Strategy

  2023cites this paper
• Comparative survey of coordinated regulation of hypothalamic-pituitary-somatotropic axis in golden pompano (Trachinotus ovatus) and humpback grouper (Cromileptes altivelis).

  2023cites this paper
• Improvements in the phylogeny of Epilobium and Chamaenerion inferred from nrDNA and cpDNA data focusing on Türkiye

  2023cites this paper
• Molecular determinants associated with temporal succession of SARS-CoV-2 variants in Uttar Pradesh, India

  2023cites this paper
• Chloroplast genomic comparison provides insights into the evolution of seagrasses

  2023cites this paper
• Early-life exposure to cigarette smoke primes lung function and DNA methylation changes at Cyp1a1 upon exposure later in life

  2023cites this paper
• Comparative analysis of mitochondrial genomes reveals marine adaptation in seagrasses

  2022cites this paper
• Molecular interaction studies of thymol via molecular dynamic simulations and free energy calculations using multi-target approach against Aedes aegypti proteome to decipher its role as mosquito repellent

  2022cites this paper
• Comprehensive Molecular Interaction Studies to Construe the Repellent/Kill Activity of Geraniol During Binding Event Against Aedes aegypti Proteins

  2022cites this paper
• Morphology and Molecular Phylogeny of Genus Oedogonium (Oedogoniales, Chlorophyta) from China

  2022cites this paper
• Bacterial matrix metalloproteases and serine proteases contribute to the extra-host inactivation of enteroviruses in lake water

  2022cites this paper
• A Hybrid Genetic Algorithm using Progressive Alignment and Consistency based Approach for Multiple Sequence Alignments

  2022influential citation
• Degradation of Alginate by a Newly Isolated Marine Bacterium Agarivorans sp. B2Z047

  2022cites this paper
• Comparative Chloroplast Genomes of Zosteraceae Species Provide Adaptive Evolution Insights Into Seagrass

  2021cites this paper
• High‐altitude adaptation in vertebrates as revealed by mitochondrial genome analyses

  2021influential citation
• Ancient Xinjiang mitogenomes reveal intense admixture with high genetic diversity

  2021cites this paper
• Comparative biogeography and the evolution of population structure for bottlenose and common dolphins in the Indian Ocean

  2021influential citation
• Selenium Yeast Dietary Supplement Affects Rumen Bacterial Population Dynamics and Fermentation Parameters of Tibetan Sheep (Ovis aries) in Alpine Meadow

  2021influential citation
• A time-calibrated multi-gene phylogeny provides insights into the evolution, taxonomy and DNA barcoding of the Pinnularia gibba group (Bacillariophyta)

  2021cites this paper
• The Afro–Oriental Genus Yaeprimus Sasa et Suzuki (Diptera: Chironomidae: Chironomini): Phylogeny, New Species and Expanded Diagnoses

  2020cites this paper
• Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach

  2020cites this paper
• In silico detection tools to identify fungal secondary metabolites and their biosynthetic gene clusters

  2020cites this paper
• First description of Weissella ceti associated with mortalities in farmed rainbow trout (Oncorhynchus mykiss) in Peru

  2020cites this paper
• Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

  2020cites this paper
• El género Herpisticus Germar, 1823 de las islas Canarias (Coleoptera: Curculionidae: Entiminae: Tanymecini)

  2020cites this paper
• New insight into the molecular mechanism of colour differentiation among floral segments in orchids

  2020cites this paper
• Phylogeny and highland adaptation of Chinese species in Allium Section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing.

  2020cites this paper
• A polyphasic approach to the delimitation of diatom species: a case study for the genus Pinnularia (Bacillariophyta)

  2019cites this paper
• A Promiscuous CYP706A3 Reduces Terpene Volatile Emission from Arabidopsis Flowers, Affecting Florivores and the Floral Microbiome[OPEN]

  2019cites this paper
• Incomer, a DD36E family of Tc1/mariner transposons newly discovered in animals

  2019influential citation
• in a

  2019cites this paper
• A phylogenetic perspective on biodiversity patterns of Afrotropical freshwater crabs (Crustacea, Decapoda, Potamonautidae)

  2019cites this paper
• Diversity, distributions, and activity of bats in the San Juan Islands

  2019influential citation
• Genomic analysis and adaptive evolution of the RIG-I-like and NOD-like receptors in reptiles.

  2019cites this paper
• Single‐base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants

  2019influential citation
• The selective constraints of ecological specialization in mustelidae on mitochondrial genomes

  2019influential citation
• Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE)

  2019cites this paper
• Diluted conventional media improve the microbial cultivability from aquarium seawater

  2019cites this paper
• Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum

  2019cites this paper
• Molecular characterization, phylogenetic analysis and adjuvant effect of channel catfish interleukin‐1&bgr;s against Streptococcus iniae

  2019cites this paper
• Aponuphis Kucheruk, 1978 (Annelida: Onuphidae) from western African waters

  2018cites this paper
• Adaptive evolution of osmoregulatory-related genes provides insight into salinity adaptation in Chinese mitten crab, Eriocheir sinensis

  2018cites this paper
• Cork Oak Young and Traumatic Periderms Show PCD Typical Chromatin Patterns but Different Chromatin-Modifying Genes Expression

  2018cites this paper
• Molecular Characterization, Phylogenetic, Expression, and Protective Immunity Analysis of OmpF, a Promising Candidate Immunogen Against Yersinia ruckeri Infection in Channel Catfish

  2018cites this paper
• Soil Bacteria Isolated From Tunisian Arid Areas Show Promising Antimicrobial Activities Against Gram-Negatives

  2018cites this paper
• EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry

  2018influential citation
• Cryptic lineage differentiation among Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the northwest Indian Ocean.

  2017cites this paper
• Laimaphelenchus suberensis sp. nov. associated with Quercus suber in Portugal

  2017cites this paper
• Reassessment of the evolutionary relationships within the dog‐faced bats, genus Cynomops (Chiroptera: Molossidae)

  2016influential citation
• Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae).

  2016cites this paper
• Phylogeography and population structure in highly mobile marine taxa in the western Indian Ocean : bottlenose dolphins (Tursiops spp.) and common dolphins (Delphinus sp.)

  2016cites this paper
• Ancestral reconstruction of reproductive traits shows no tendency toward terrestriality in leptodactyline frogs

  2015cites this paper
• Comparative phylogeography of five bumblebees: Impact of range fragmentation, range size and diet specialization

  2015influential citation
• Phylogenetic congruence of parasitic smut fungi (Anthracoidea, Anthracoideaceae) and their host plants (Carex, Cyperaceae): Cospeciation or host-shift speciation?

  2015cites this paper
• Investigating Intra-and InterMolecular Coevolution of Intrinsically Disordered Protein , Prothymosin-α

  2015cites this paper
• Impact of past climatic changes and resource availability on the population demography of three food‐specialist bees

  2015influential citation
• Lachancea quebecensis sp. nov., a yeast species consistently isolated from tree bark in the Canadian province of Québec.

  2015cites this paper
• Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem

  2015cites this paper
• Automated Software Debugging Using Hybrid Static/Dynamic Analysis

  2015cites this paper
• AN ITERATIVE APPROACH FOR EVALUATING THE ALIGNMENT QUALITY OF MULTIPLE BIOLOGICAL SEQUENCES

  2015cites this paper
• Assessment of genetic structure, habitat suitability and effectiveness of reserves for future conservation planning of the Euphrates soft‐shelled turtle Rafetus euphraticus (Daudin, 1802)

  2014cites this paper
• Molecular phylogeny, biogeography, and host plant shifts in the bee genus Melitta (Hymenoptera: Anthophila).

  2014cites this paper
• Coevolution signals capture the specific packing of secondary structures in protein architecture

  2014influential citation
• MOLECULAR SYSTEMATICS OF SELECTED GENERA OF SUBFAMILY MIMOSOIDEAE-FABACEAE

  2014influential citation
• Negative and positive contributions of arbuscular mycorrhizal fungal taxa to wheat production and nutrient uptake efficiency in organic and conventional systems in the Canadian prairie

  2014cites this paper
• New occurrences of Botryosphaeriaceae causing black root rot of cassava in Brazil

  2014cites this paper
• Inferring the mode of colonization of the rapid range expansion of a solitary bee from multilocus DNA sequence variation

  2014influential citation
• A review of the currently recognised zoogonid cercariae, including the identification and emergence ecology of Cercaria capricornia XI (Digenea: Zoogonidae) from Nassarius olivaceus (Gastropoda: Nassariidae) in Central Queensland, Australia.

  2014influential citation
• INFERRING THE PAST AND PRESENT CONNECTIVITY ACROSS THE RANGE OF A NORTH AMERICAN LEAF BEETLE: COMBINING ECOLOGICAL NICHE MODELING AND A GEOGRAPHICALLY EXPLICIT MODEL OF COALESCENCE

  2014cites this paper
• Population Genomic Analysis Reveals Highly Conserved Mitochondrial Genomes in the Yeast Species Lachancea thermotolerans

  2014cites this paper
• Molecular evolution of calcification genes in morphologically similar but phylogenetically unrelated scleractinian corals.

  2014cites this paper
• Impact of Land Use on Arbuscular Mycorrhizal Fungal Communities in Rural Canada

  2013cites this paper
• Title: Impact of land use on arbuscular mycorrhizal fungal communities in rural

  2013cites this paper
• Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia

  2013cites this paper
• Structure, Diversity, and Mobility of the Salmonella Pathogenicity Island 7 Family of Integrative and Conjugative Elements within Enterobacteriaceae

  2012cites this paper
• Molecular ecology and evolution of reef corals and their algal symbionts

  2012influential citation
• Selecting ribosomal protein genes for invertebrate phylogenetic inferences: how many genes to resolve the Mollusca?

  2011influential citation
• Indications of sexual reproduction in microsporidia

  2011cites this paper
• First description of algal mutualistic endosymbiosis in a black coral (Anthozoa: Antipatharia)

  2011cites this paper
• Respiratory proteins in Sipunculus nudus--implications for phylogeny and evolution of the hemerythrin family.

  2010cites this paper
• Chasing organohalide respirers: ecogenomics approaches to assess the bioremediation capacity of soils

  2010cites this paper
• Coral systematics inferred from the gene galaxin : Exploring phylogenetic relationships using a putative determinant of skeletal morphology

  2009cites this paper
• Multiple DNA sequence alignment based on genetic simulated annealing techniques

  2007cites this paper
• Molecular taxonomy in pholcid spiders ( Pholcidae , Araneae ) : evaluation of species identification methods using CO 1 and 16 S rRNA

  2006cites this paper
• Molecular biology and genetics/Biologie et ge´ne´tique mole´culaires Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (

  year unknowninfluential citation