Published in Bioinformatics on March 01, 2002
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods (2013) 31.15
Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res (2004) 28.63
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res (2004) 8.58
Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics (2005) 7.01
SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics (2012) 6.40
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci (2010) 6.39
Fast statistical alignment. PLoS Comput Biol (2009) 5.92
De novo repeat classification and fragment assembly. Genome Res (2004) 4.58
M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res (2006) 4.53
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol (2015) 3.66
Complete genome sequence of Kytococcus sedentarius type strain (541). Stand Genomic Sci (2009) 3.30
Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol (2007) 3.29
A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res (2005) 2.89
A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res (2004) 2.73
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics (2009) 2.64
A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods (2015) 2.52
The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics (2006) 2.52
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res (2004) 2.46
Finding functional sequence elements by multiple local alignment. Nucleic Acids Res (2004) 2.37
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol (2006) 2.35
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol Biol (2008) 2.07
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics (2012) 2.07
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res (2010) 2.05
Cactus: Algorithms for genome multiple sequence alignment. Genome Res (2011) 2.03
Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97
Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci (2010) 1.96
Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res (2004) 1.93
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res (2006) 1.90
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics (2005) 1.87
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res (2007) 1.84
Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci (2009) 1.82
Widely conserved recombination patterns among single-stranded DNA viruses. J Virol (2008) 1.78
Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA (2007) 1.75
The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res (2004) 1.70
Current challenges in de novo plant genome sequencing and assembly. Genome Biol (2012) 1.69
A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One (2011) 1.65
Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog (2007) 1.62
A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family. Plant Physiol (2003) 1.60
Identifying repeat domains in large genomes. Genome Biol (2006) 1.58
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol (2016) 1.57
Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol (2010) 1.56
Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes). BMC Evol Biol (2006) 1.40
Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing. Genome Biol Evol (2011) 1.39
Improved genome inference in the MHC using a population reference graph. Nat Genet (2015) 1.38
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects. Stand Genomic Sci (2013) 1.35
Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255). Stand Genomic Sci (2009) 1.34
Complete genome sequence of Spirosoma linguale type strain (1). Stand Genomic Sci (2010) 1.32
The evolutionary value of recombination is constrained by genome modularity. PLoS Genet (2005) 1.26
The conversion of 3' UTRs into coding regions. Mol Biol Evol (2006) 1.24
Assessing the efficiency of multiple sequence alignment programs. Algorithms Mol Biol (2014) 1.23
Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci (2010) 1.21
Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res (2006) 1.21
Multiple sequence alignment with user-defined anchor points. Algorithms Mol Biol (2006) 1.20
Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Stand Genomic Sci (2009) 1.17
Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora. PLoS One (2009) 1.16
Complete genome sequence of Segniliparus rotundus type strain (CDC 1076). Stand Genomic Sci (2010) 1.15
Twenty-Five New Viruses Associated with the Drosophilidae (Diptera). Evol Bioinform Online (2016) 1.14
Complete genome sequence of Atopobium parvulum type strain (IPP 1246). Stand Genomic Sci (2009) 1.14
FAST DB: a website resource for the study of the expression regulation of human gene products. Nucleic Acids Res (2005) 1.14
Complete genome sequence of Cryptobacterium curtum type strain (12-3). Stand Genomic Sci (2009) 1.12
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA. Evol Bioinform Online (2010) 1.12
Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Stand Genomic Sci (2010) 1.10
A systematic search for positive selection in higher plants (Embryophytes). BMC Plant Biol (2006) 1.10
Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Stand Genomic Sci (2011) 1.08
Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Mol Biol Evol (2009) 1.08
hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics (2015) 1.08
Complete genome sequence of Saccharomonospora viridis type strain (P101). Stand Genomic Sci (2009) 1.07
An ORFome assembly approach to metagenomics sequences analysis. J Bioinform Comput Biol (2009) 1.07
Complete genome sequence of Haloterrigena turkmenica type strain (4k). Stand Genomic Sci (2010) 1.06
Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Stand Genomic Sci (2011) 1.06
Comparing sequences without using alignments: application to HIV/SIV subtyping. BMC Bioinformatics (2007) 1.05
A phylogenetic study of cytochrome b561 proteins. Genome Biol (2003) 1.05
Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci (2012) 1.05
Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1). Stand Genomic Sci (2009) 1.04
A highly divergent gene cluster in honey bees encodes a novel silk family. Genome Res (2006) 1.01
Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). Stand Genomic Sci (2011) 1.01
Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122). Stand Genomic Sci (2009) 1.00
Complete genome sequence of Sulfurimonas autotrophica type strain (OK10). Stand Genomic Sci (2010) 1.00
Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Stand Genomic Sci (2009) 1.00
Contact-based sequence alignment. Nucleic Acids Res (2004) 0.99
Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)). Stand Genomic Sci (2011) 0.99
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
Complete genome sequence of Dyadobacter fermentans type strain (NS114). Stand Genomic Sci (2009) 0.99
Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Stand Genomic Sci (2011) 0.99
Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Stand Genomic Sci (2010) 0.99
Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Stand Genomic Sci (2010) 0.99
Complete genome sequence of Planctomyces limnophilus type strain (Mü 290). Stand Genomic Sci (2010) 0.98
Complete genome sequence of Anaerococcus prevotii type strain (PC1). Stand Genomic Sci (2009) 0.97
Complete genome sequence of Halomicrobium mukohataei type strain (arg-2). Stand Genomic Sci (2009) 0.97
Complete genome sequence of Desulfomicrobium baculatum type strain (X). Stand Genomic Sci (2009) 0.97
Complete genome sequence of Paludibacter propionicigenes type strain (WB4). Stand Genomic Sci (2011) 0.97
Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Stand Genomic Sci (2011) 0.96
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. Nucleic Acids Res (2006) 0.96
Complete genome sequence of Gordonia bronchialis type strain (3410). Stand Genomic Sci (2010) 0.96
Complete genome sequence of Thermosphaera aggregans type strain (M11TL). Stand Genomic Sci (2010) 0.96
Complete genome sequence of Isosphaera pallida type strain (IS1B). Stand Genomic Sci (2011) 0.96
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res (2011) 1.63
Computational analysis of sequence selection mechanisms. Structure (2004) 0.95