Published in Mol Biol Evol on April 01, 2000
Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res (2008) 19.09
Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut (2005) 10.95
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Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. MBio (2012) 8.54
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res (2006) 8.36
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol (2013) 6.40
Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5.79
A simple, fast, and accurate method of phylogenomic inference. Genome Biol (2008) 5.47
Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol (2010) 5.33
ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res (2010) 5.32
The Amphimedon queenslandica genome and the evolution of animal complexity. Nature (2010) 5.11
Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc Biol Sci (2009) 5.08
Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A (2005) 4.37
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol (2006) 4.03
Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii. BMC Genomics (2010) 4.03
Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol (2011) 3.89
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res (2010) 3.83
The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci U S A (2003) 3.81
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol (2009) 3.63
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res (2002) 3.41
Using the Acropora digitifera genome to understand coral responses to environmental change. Nature (2011) 3.26
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet (2008) 3.23
Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature (2011) 3.06
Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins. Genome Biol (2006) 2.99
Single-copy nuclear genes resolve the phylogeny of the holometabolous insects. BMC Biol (2009) 2.99
The ctenophore genome and the evolutionary origins of neural systems. Nature (2014) 2.96
GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res (2010) 2.95
Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe (2012) 2.66
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog (2012) 2.66
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol (2010) 2.58
ADP-glucose pyrophosphorylase is activated by posttranslational redox-modification in response to light and to sugars in leaves of Arabidopsis and other plant species. Plant Physiol (2003) 2.55
A robust species tree for the alphaproteobacteria. J Bacteriol (2007) 2.54
Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci U S A (2006) 2.47
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res (2006) 2.42
An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol (2010) 2.39
Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella. Infect Immun (2008) 2.38
The archaebacterial origin of eukaryotes. Proc Natl Acad Sci U S A (2008) 2.36
Phylogenetic and ecological analysis of novel marine stramenopiles. Appl Environ Microbiol (2004) 2.35
Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol Biol Evol (2008) 2.33
Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria. BMC Evol Biol (2008) 2.21
Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A (2014) 2.20
Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens. PLoS One (2015) 2.15
Evolution of microgastropods (Ellobioidea, Carychiidae): integrating taxonomic, phylogenetic and evolutionary hypotheses. BMC Evol Biol (2013) 2.11
The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii. PLoS Genet (2008) 2.10
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res (2009) 2.10
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol (2012) 2.08
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol (2008) 2.06
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature (2011) 2.01
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res (2010) 2.00
A glimpse on the pattern of rodent diversification: a phylogenetic approach. BMC Evol Biol (2012) 2.00
Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol (2010) 2.00
Origins and diversification of a complex signal transduction system in prokaryotes. Sci Signal (2010) 1.98
Comparative genomics of protoploid Saccharomycetaceae. Genome Res (2009) 1.96
Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci (2010) 1.96
Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci U S A (2006) 1.94
OrthoDB: the hierarchical catalog of eukaryotic orthologs. Nucleic Acids Res (2007) 1.91
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol (2013) 1.87
The genome sequence of the colonial chordate, Botryllus schlosseri. Elife (2013) 1.86
On the origin of Acochlidia and other enigmatic euthyneuran gastropods, with implications for the systematics of Heterobranchia. BMC Evol Biol (2010) 1.85
Numerous transitions of sex chromosomes in Diptera. PLoS Biol (2015) 1.85
The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One (2010) 1.84
Phylogeny, evolution, and biogeography of Asiatic Salamanders (Hynobiidae). Proc Natl Acad Sci U S A (2006) 1.83
Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci (2009) 1.82
Independent evolution of striated muscles in cnidarians and bilaterians. Nature (2012) 1.81
Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. PLoS One (2010) 1.81
Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster. Appl Environ Microbiol (2007) 1.80
Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes. BMC Evol Biol (2009) 1.78
Evolution of box jellyfish (Cnidaria: Cubozoa), a group of highly toxic invertebrates. Proc Biol Sci (2009) 1.77
SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol (2007) 1.76
Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol (2009) 1.76
Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell (2016) 1.76
Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J (2013) 1.76
Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS One (2012) 1.75
PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol (2007) 1.74
A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals. Elife (2012) 1.72
The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis. Genome Biol Evol (2012) 1.71
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A (2014) 1.70
A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ Microbiol (2010) 1.70
Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Res (2012) 1.69
An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. PLoS One (2007) 1.67
Description of Leptopharynx bromelicola n. sp. and characterization of the genus Leptopharynx Mermod, 1914 (Protista, Ciliophora). J Eukaryot Microbiol (2011) 1.67
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol (2015) 1.66
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. Genome Res (2003) 1.65
Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. J Bacteriol (2009) 1.64
Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci (2008) 1.64
Functions, structure, and read-through alternative splicing of feline APOBEC3 genes. Genome Biol (2008) 1.63
Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol Biol Evol (2011) 1.62
Novel, divergent simian hemorrhagic fever viruses in a wild Ugandan red colobus monkey discovered using direct pyrosequencing. PLoS One (2011) 1.62
Complete genome sequence of Macrococcus caseolyticus strain JCSCS5402, [corrected] reflecting the ancestral genome of the human-pathogenic staphylococci. J Bacteriol (2008) 1.61
Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J (2014) 1.60
Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proc Natl Acad Sci U S A (2014) 1.59
Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol (2008) 1.59
Melatonin signaling controls circadian swimming behavior in marine zooplankton. Cell (2014) 1.59
Genome-wide signatures of convergent evolution in echolocating mammals. Nature (2013) 1.59
Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis. Genome Res (2006) 1.58
Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes. BMC Microbiol (2011) 1.58
An expanded genomic representation of the phylum cyanobacteria. Genome Biol Evol (2014) 1.56
Orthology prediction methods: a quality assessment using curated protein families. Bioessays (2011) 1.56
Exceptional simian hemorrhagic fever virus diversity in a wild African primate community. J Virol (2012) 1.53