Published in Nucleic Acids Res on July 01, 1999
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res (2002) 47.62
Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res (2004) 28.63
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One (2010) 24.31
ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res (2005) 11.90
Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics (2005) 7.01
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res (2001) 6.67
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res (2000) 5.70
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res (2003) 4.97
Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics (2004) 4.00
A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics (2004) 3.20
GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res (2010) 2.95
A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res (2005) 2.89
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res (2004) 2.46
A method for prediction of the locations of linker regions within large multifunctional proteins, and application to a type I polyketide synthase. J Mol Biol (2002) 2.41
An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol (2010) 2.39
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol (2006) 2.35
SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One (2014) 2.33
Toward a comprehensive phylogeny for mammalian and avian herpesviruses. J Virol (2000) 2.17
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res (2010) 2.05
Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics (2006) 1.92
Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res (2003) 1.88
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics (2005) 1.87
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res (2006) 1.85
Gene mention normalization and interaction extraction with context models and sentence motifs. Genome Biol (2008) 1.83
On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J (2006) 1.79
PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments. BMC Bioinformatics (2007) 1.71
A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One (2011) 1.65
Identification and analysis of amino acid mutations in porin IB that mediate intermediate-level resistance to penicillin and tetracycline in Neisseria gonorrhoeae. Antimicrob Agents Chemother (2002) 1.63
Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS One (2009) 1.62
PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res (2008) 1.58
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics (2006) 1.44
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. BMC Bioinformatics (2008) 1.35
Accounting for alignment uncertainty in phylogenomics. PLoS One (2012) 1.35
Molecular identification of enterovirus by analyzing a partial VP1 genomic region with different methods. J Clin Microbiol (2002) 1.33
High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes. Genome Res (2011) 1.32
Formation of the Arabidopsis pentatricopeptide repeat family. Plant Physiol (2006) 1.28
Comparative analysis of protein structure alignments. BMC Struct Biol (2007) 1.28
Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc Natl Acad Sci U S A (2004) 1.25
Assessing the efficiency of multiple sequence alignment programs. Algorithms Mol Biol (2014) 1.23
A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics (2008) 1.23
Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. BMC Genomics (2006) 1.21
Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res (2006) 1.21
Multiple sequence alignment: a major challenge to large-scale phylogenetics. PLoS Curr (2010) 1.20
PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res (2007) 1.20
Multiple sequence alignment with user-defined anchor points. Algorithms Mol Biol (2006) 1.20
Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evol Biol (2006) 1.18
Do constructional constraints influence cichlid craniofacial diversification? Proc Biol Sci (2007) 1.13
A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci (2002) 1.13
A system for automated lexical mapping. J Am Med Inform Assoc (2006) 1.11
Sequence analysis of two cryptic plasmids from Bifidobacterium longum DJO10A and construction of a shuttle cloning vector. Appl Environ Microbiol (2006) 1.10
Evolution and phylogeny of insect endogenous retroviruses. BMC Evol Biol (2001) 1.07
Paleodistributions and comparative molecular phylogeography of leafcutter ants (Atta spp.) provide new insight into the origins of Amazonian diversity. PLoS One (2008) 1.06
Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics (2005) 1.06
A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities. BMC Bioinformatics (2005) 1.04
LEON: multiple aLignment Evaluation Of Neighbours. Nucleic Acids Res (2004) 1.04
Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylase. BMC Evol Biol (2009) 1.04
Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics (2005) 1.03
Signal processing for metagenomics: extracting information from the soup. Curr Genomics (2009) 1.02
Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3. ISME J (2010) 1.02
WAR: Webserver for aligning structural RNAs. Nucleic Acids Res (2008) 1.01
Molecular epidemiology of foot-and-mouth disease viruses in the Adamawa province of Cameroon. J Clin Microbiol (2004) 1.01
Multi-species sequence comparison: the next frontier in genome annotation. Genome Biol (2003) 1.00
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biol (2007) 0.99
A new protein linear motif benchmark for multiple sequence alignment software. BMC Bioinformatics (2008) 0.99
The peroxidase gene family in plants: a phylogenetic overview. J Mol Evol (2003) 0.98
A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinformatics (2006) 0.98
Affinity of aporphines for the human 5-HT2A receptor: insights from homology modeling and molecular docking studies. Bioorg Med Chem (2010) 0.95
Accuracy analysis of multiple structure alignments. Protein Sci (2009) 0.95
Improvement of alignment accuracy utilizing sequentially conserved motifs. BMC Bioinformatics (2004) 0.94
Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS One (2012) 0.94
Phylogenetic ubiquity and shuffling of the bacterial RecBCD and AddAB recombination complexes. J Bacteriol (2009) 0.93
DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors. BMC Bioinformatics (2004) 0.93
How accurately is ncRNA aligned within whole-genome multiple alignments? BMC Bioinformatics (2007) 0.92
BCL::Align-sequence alignment and fold recognition with a custom scoring function online. Gene (2008) 0.90
The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis. BMC Plant Biol (2008) 0.89
Reevaluation of the evolutionary position of opalinids based on 18S rDNA, and alpha- and beta-tubulin gene phylogenies. J Mol Evol (2005) 0.89
Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res (2008) 0.89
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases. BMC Bioinformatics (2002) 0.89
Homology modeling a fast tool for drug discovery: current perspectives. Indian J Pharm Sci (2012) 0.87
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. BMC Bioinformatics (2011) 0.87
A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule. BMC Biol (2016) 0.86
Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences. BMC Bioinformatics (2003) 0.86
SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation. BMC Bioinformatics (2011) 0.86
Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees. Bioinformatics (2016) 0.86
Hybrid homology modeling and mutational analysis of cytochrome P450C24A1 (CYP24A1) of the Vitamin D pathway: insights into substrate specificity and membrane bound structure-function. Arch Biochem Biophys (2006) 0.85
Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes. PLoS Comput Biol (2015) 0.85
First molecular determination of herpesvirus from two mysticete species stranded in the Mediterranean Sea. BMC Vet Res (2015) 0.85
SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches. Nucleic Acids Res (2009) 0.84
Evolutionary dynamics of the Pgk1 gene in the polyploid genus Kengyilia (Triticeae: Poaceae) and its diploid relatives. PLoS One (2012) 0.84
DivA: detection of non-homologous and very divergent regions in protein sequence alignments. BMC Res Notes (2014) 0.83
Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes. Nucleic Acids Res (2013) 0.82
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. BMC Bioinformatics (2014) 0.82
Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms Mol Biol (2008) 0.81
Strategies for reliable exploitation of evolutionary concepts in high throughput biology. Evol Bioinform Online (2008) 0.81
Statistical power of phylo-HMM for evolutionarily conserved element detection. BMC Bioinformatics (2007) 0.81
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map. BMC Bioinformatics (2016) 0.80
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res (1997) 175.36
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics (1999) 12.64
Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature (1990) 9.21
An attempt to unify the structure of polymerases. Protein Eng (1990) 7.93
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res (2001) 6.67
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res (2000) 5.70
Walking along the rabies genome: is the large G-L intergenic region a remnant gene? Proc Natl Acad Sci U S A (1986) 3.49
Towards a reliable objective function for multiple sequence alignments. J Mol Biol (2001) 3.07
Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene (2001) 2.88
Rift Valley fever virus L segment: correction of the sequence and possible functional role of newly identified regions conserved in RNA-dependent polymerases. J Gen Virol (1994) 2.84
RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics (2003) 2.79
Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea. Genome Res (2001) 2.64
Completion of the rabies virus genome sequence determination: highly conserved domains among the L (polymerase) proteins of unsegmented negative-strand RNA viruses. Virology (1988) 2.02
Human TAF(II)28 and TAF(II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family. Cell (1998) 1.63
Secator: a program for inferring protein subfamilies from phylogenetic trees. Mol Biol Evol (2001) 1.57
Head and neck squamous cell carcinoma transcriptome analysis by comprehensive validated differential display. Oncogene (2006) 1.56
Primary structure of leader RNA and nucleoprotein genes of the rabies genome: segmented homology with VSV. Nucleic Acids Res (1986) 1.53
The human TFIID components TAF(II)135 and TAF(II)20 and the yeast SAGA components ADA1 and TAF(II)68 heterodimerize to form histone-like pairs. Mol Cell Biol (2000) 1.45
Structure and function of poly(ADP-ribose) polymerase. Mol Cell Biochem (1994) 1.38
GOAnno: GO annotation based on multiple alignment. Bioinformatics (2005) 1.34
The TBP-like factor: an alternative transcription factor in metazoa? Trends Biochem Sci (1999) 1.33
Identification of 28 novel mutations in the Bardet-Biedl syndrome genes: the burden of private mutations in an extensively heterogeneous disease. Hum Genet (2010) 1.33
Expression and site-directed mutagenesis of the catalytic domain of human poly(ADP-ribose)polymerase in Escherichia coli. Lysine 893 is critical for activity. J Biol Chem (1990) 1.22
The 'PINIT' motif, of a newly identified conserved domain of the PIAS protein family, is essential for nuclear retention of PIAS3L. FEBS Lett (2003) 1.18
Identification of potential active-site residues in the human poly(ADP-ribose) polymerase. J Biol Chem (1993) 1.15
Ballast: blast post-processing based on locally conserved segments. Bioinformatics (2000) 1.13
Mu-opioid receptor activation induces transcriptional plasticity in the central extended amygdala. Eur J Neurosci (2008) 1.12
The disruption of the rod-derived cone viability gene leads to photoreceptor dysfunction and susceptibility to oxidative stress. Cell Death Differ (2010) 1.08
SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr (2006) 1.08
Transcriptome analysis identifies genes with enriched expression in the mouse central extended amygdala. Neuroscience (2008) 1.07
Synergistic transcriptional activation by TATA-binding protein and hTAFII28 requires specific amino acids of the hTAFII28 histone fold. Mol Cell Biol (1999) 1.04
DbW: automatic update of a functional family-specific multiple alignment. Bioinformatics (2004) 0.98
Time-resolved analysis of transcriptional events during SNAI1-triggered epithelial to mesenchymal transition. Biochem Biophys Res Commun (2009) 0.93
Gene expression is altered in the lateral hypothalamus upon activation of the mu opioid receptor. Ann N Y Acad Sci (2008) 0.91
The microdistribution of isoenzymic strains of Trypanosoma cruzi in southern Bolivia; new isoenzyme profiles and further arguments against Mendelian sexuality. Trans R Soc Trop Med Hyg (1984) 0.91
A eukaryotic XPB/ERCC3-like helicase in Mycobacterium leprae? Trends Biochem Sci (1997) 0.83
Décrypthon grid - grid resources dedicated to neuromuscular disorders. Stud Health Technol Inform (2010) 0.83
The archaeal homolog of the Imp4 protein, a eukaryotic U3 snoRNP component. Trends Biochem Sci (2001) 0.83
Analysis of the structural diversity of monoclonal antibodies to cyclosporine. Mol Immunol (1990) 0.76
Functional and structural analysis of the subunits of human transcription factor TFIID. Cold Spring Harb Symp Quant Biol (1998) 0.76
MAGOS: multiple alignment and modelling server. Bioinformatics (2006) 0.75
[The early detection by magnetic resonance of bone infiltration in HIV-related lymphomas]. Med Clin (Barc) (1994) 0.75
Additional data on Trypanosoma cruzi isozymic strains encountered in Bolivian domestic transmission cycles. Trans R Soc Trop Med Hyg (1986) 0.75
Specific humoral depression in chronic patients infected by Trypanosoma cruzi. Rev Inst Med Trop Sao Paulo (1985) 0.75
[100 years later...the rabies virus]. Bull Acad Natl Med (1987) 0.75
Analysis of a 22,956 bp region on the right arm of Saccharomyces cerevisiae chromosome XV. Yeast (1996) 0.75
Chagas serology and its problems. Ann Soc Belg Med Trop (1985) 0.75
Analysis of a 35.6 kb region on the right arm of Saccharomyces cerevisiae chromosome XV. Yeast (1997) 0.75
The fate of aerosols on the surface of Titan. Faraday Discuss (2010) 0.75