Published in Mol Biol Evol on March 26, 2008
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res (2010) 9.68
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics (2010) 5.70
phangorn: phylogenetic analysis in R. Bioinformatics (2010) 4.57
Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature (2010) 4.35
INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol (2009) 3.29
Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol (2009) 2.55
Phylogeny of gammaproteobacteria. J Bacteriol (2010) 2.35
Analysis of Drosophila TRPA1 reveals an ancient origin for human chemical nociception. Nature (2010) 2.35
Origin of land plants: do conjugating green algae hold the key? BMC Evol Biol (2011) 2.04
Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature (2011) 2.01
T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res (2012) 1.97
DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. Biotechniques (2010) 1.88
ALF--a simulation framework for genome evolution. Mol Biol Evol (2011) 1.86
A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans. PLoS Biol (2011) 1.84
Pheophytin pheophorbide hydrolase (pheophytinase) is involved in chlorophyll breakdown during leaf senescence in Arabidopsis. Plant Cell (2009) 1.68
A gustatory receptor paralogue controls rapid warmth avoidance in Drosophila. Nature (2013) 1.67
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol (2015) 1.66
Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol Biol Evol (2011) 1.62
Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PLoS Genet (2014) 1.61
CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol (2010) 1.56
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans. Nat Genet (2013) 1.52
FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res (2012) 1.52
Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci U S A (2015) 1.51
The Apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees. Mol Biol Evol (2008) 1.48
The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME J (2012) 1.48
Genetic and phenotypic characterization of GII-4 noroviruses that circulated during 1987 to 2008. J Virol (2010) 1.46
RSL Class I Genes Controlled the Development of Epidermal Structures in the Common Ancestor of Land Plants. Curr Biol (2015) 1.45
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi. BMC Biol (2012) 1.45
Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci (2008) 1.45
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG). Nature (2010) 1.44
A comprehensive analysis of the La-motif protein superfamily. RNA (2009) 1.44
The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genet (2012) 1.43
The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol (2016) 1.42
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res (2014) 1.42
Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PLoS One (2016) 1.40
Characterization of the Drosophila group ortholog to the amino-terminus of the alpha-thalassemia and mental retardation X-Linked (ATRX) vertebrate protein. PLoS One (2014) 1.40
The two-domain tree of life is linked to a new root for the Archaea. Proc Natl Acad Sci U S A (2015) 1.39
Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol Biol (2010) 1.39
Heat avoidance is regulated by transient receptor potential (TRP) channels and a neuropeptide signaling pathway in Caenorhabditis elegans. Genetics (2011) 1.37
Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee. Proc Natl Acad Sci U S A (2012) 1.37
The gene YALI0E20207g from Yarrowia lipolytica encodes an N-acetylglucosamine kinase implicated in the regulated expression of the genes from the N-acetylglucosamine assimilatory pathway. PLoS One (2015) 1.37
A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants. Philos Trans R Soc Lond B Biol Sci (2010) 1.33
Phylogenomic data support a seventh order of Methylotrophic methanogens and provide insights into the evolution of Methanogenesis. Genome Biol Evol (2013) 1.33
Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in spiroplasma. Genome Biol Evol (2013) 1.32
New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias. BMC Evol Biol (2013) 1.32
Genomic data do not support comb jellies as the sister group to all other animals. Proc Natl Acad Sci U S A (2015) 1.31
Molecular evolution of the junctophilin gene family. Physiol Genomics (2009) 1.31
Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding. PLoS Genet (2012) 1.27
An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiol (2012) 1.26
The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evol Biol (2014) 1.25
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res (2015) 1.25
Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. ISME J (2013) 1.23
O-GlcNAc protein modification in plants: Evolution and function. Biochim Biophys Acta (2009) 1.23
Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. BMC Biol (2012) 1.23
Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics (2013) 1.23
Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum. BMC Genomics (2010) 1.20
Efficient exploration of the space of reconciled gene trees. Syst Biol (2013) 1.20
Molecular evolution of peptidergic signaling systems in bilaterians. Proc Natl Acad Sci U S A (2013) 1.19
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res (2016) 1.18
Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol (2013) 1.18
Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton. BMC Evol Biol (2010) 1.17
Construction and validation of a homology model of the human voltage-gated proton channel hHV1. J Gen Physiol (2013) 1.17
Ancient diversification of eukaryotic MCM DNA replication proteins. BMC Evol Biol (2009) 1.17
Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biol Evol (2013) 1.16
Twenty-Five New Viruses Associated with the Drosophilidae (Diptera). Evol Bioinform Online (2016) 1.14
Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. BMC Genomics (2012) 1.14
CREST--a large and diverse superfamily of putative transmembrane hydrolases. Biol Direct (2011) 1.12
Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS One (2011) 1.11
A consistent phylogenetic backbone for the fungi. Mol Biol Evol (2011) 1.11
Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol (2013) 1.10
A cell-surface phylome for African trypanosomes. PLoS Negl Trop Dis (2013) 1.09
The mammalian PYHIN gene family: phylogeny, evolution and expression. BMC Evol Biol (2012) 1.09
Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches. BMC Biol (2011) 1.09
Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us. PLoS Negl Trop Dis (2013) 1.09
Ribonucleotide reduction - horizontal transfer of a required function spans all three domains. BMC Evol Biol (2010) 1.09
DNA-binding specificity changes in the evolution of forkhead transcription factors. Proc Natl Acad Sci U S A (2013) 1.08
Conserved meiotic machinery in Glomus spp., a putatively ancient asexual fungal lineage. Genome Biol Evol (2011) 1.08
Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria. MBio (2013) 1.07
Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. ISME J (2011) 1.07
Evolution of the MAGUK protein gene family in premetazoan lineages. BMC Evol Biol (2010) 1.07
Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates. Proc Natl Acad Sci U S A (2010) 1.07
A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol Biol (2008) 1.06
Doing it in reverse: 3'-to-5' polymerization by the Thg1 superfamily. RNA (2012) 1.05
Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS One (2014) 1.05
Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner. PLoS Genet (2015) 1.05
Complete sequence of the mitochondrial genome of a diatom alga Synedra acus and comparative analysis of diatom mitochondrial genomes. Curr Genet (2010) 1.04
The evolutionary origins of detoxifying enzymes: the mammalian serum paraoxonases (PONs) relate to bacterial homoserine lactonases. J Biol Chem (2013) 1.04
Differential loss and retention of cytoglobin, myoglobin, and globin-E during the radiation of vertebrates. Genome Biol Evol (2011) 1.04
An expressed sequence tag analysis of the intertidal brown seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in response to abiotic stressors. Mar Biotechnol (NY) (2009) 1.03
Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proc Biol Sci (2013) 1.03
Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses. PLoS One (2011) 1.03
Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids. Mol Phylogenet Evol (2013) 1.02
Evolution and classification of myosins, a paneukaryotic whole-genome approach. Genome Biol Evol (2014) 1.02
Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics (2015) 1.02
Archaeal "dark matter" and the origin of eukaryotes. Genome Biol Evol (2014) 1.02
Infectious endogenous retroviruses in cats and emergence of recombinant viruses. J Virol (2012) 1.01
Gibberellin metabolism in Vitis vinifera L. during bloom and fruit-set: functional characterization and evolution of grapevine gibberellin oxidases. J Exp Bot (2013) 1.00
Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol (2012) 1.00
Evolutionary patterns in coiled-coils. Genome Biol Evol (2015) 1.00
Basic leucine zipper protein Cnc-C is a substrate and transcriptional regulator of the Drosophila 26S proteasome. Mol Cell Biol (2010) 0.99
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol (2009) 21.24
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol (2006) 12.96
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res (2005) 8.20
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol (2002) 5.50
Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol (2009) 5.12
Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol Biol Evol (2012) 3.35
Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol Biol Evol (2003) 3.26
Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics (2005) 2.70
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol (2011) 2.66
Genomics, biogeography, and the diversification of placental mammals. Proc Natl Acad Sci U S A (2007) 1.86
Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Trans Comput Biol Bioinform (2009) 1.58
Identification of novel peptide hormones in the human proteome by hidden Markov model screening. Genome Res (2007) 1.50
Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci (2008) 1.45
Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics (2008) 1.43
SDM: a fast distance-based approach for (super) tree building in phylogenomics. Syst Biol (2006) 1.36
Duplication and inversion history of a tandemly repeated genes family. J Comput Biol (2007) 1.22
Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Mol Biol Evol (2002) 1.14
Reconstructing the duplication history of tandemly repeated genes. Mol Biol Evol (2002) 1.08
Branch lengths on birth-death trees and the expected loss of phylogenetic diversity. Syst Biol (2011) 0.97
Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial. Syst Biol (2010) 0.96
Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets. Mol Biol Evol (2002) 0.96
PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data. BMC Bioinformatics (2008) 0.93
A fast and specific alignment method for minisatellite maps. Evol Bioinform Online (2007) 0.92
Detection of new protein domains using co-occurrence: application to Plasmodium falciparum. Bioinformatics (2009) 0.91
Getting a tree fast: Neighbor Joining, FastME, and distance-based methods. Curr Protoc Bioinformatics (2006) 0.91
Deep conservation of human protein tandem repeats within the eukaryotes. Mol Biol Evol (2014) 0.91
FLU, an amino acid substitution model for influenza proteins. BMC Evol Biol (2010) 0.91
Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinformatics (2005) 0.90
Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics (2008) 0.90
The origin and evolutionary history of HIV-1 subtype C in Senegal. PLoS One (2012) 0.89
Searching for virus phylotypes. Bioinformatics (2013) 0.89
A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK. AIDS (2015) 0.87
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees. Bioinformatics (2002) 0.87
Combinatorics of distance-based tree inference. Proc Natl Acad Sci U S A (2012) 0.83
Sexually-transmitted/founder HIV-1 cannot be directly predicted from plasma or PBMC-derived viral quasispecies in the transmitting partner. PLoS One (2013) 0.83
A simple method to predict protein-binding from aligned sequences--application to MHC superfamily and beta2-microglobulin. Bioinformatics (2005) 0.83
Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum. BMC Genomics (2010) 0.82
ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices. Bioinformatics (2011) 0.81
The behavior of admixed populations in neighbor-joining inference of population trees. Pac Symp Biocomput (2013) 0.81
EuPathDomains: the divergent domain database for eukaryotic pathogens. Infect Genet Evol (2010) 0.80
A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism. BMC Genomics (2009) 0.79
Using repeated measurements to validate hierarchical gene clusters. Bioinformatics (2008) 0.79
Topological rearrangements and local search method for tandem duplication trees. IEEE/ACM Trans Comput Biol Bioinform (2006) 0.78
Robustness of phylogenetic inference based on minimum evolution. Bull Math Biol (2010) 0.78
Computational discovery of regulatory elements in a continuous expression space. Genome Biol (2012) 0.77
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. BMC Bioinformatics (2012) 0.77
Bamako 2009 conference on the bioinformatics of infectious diseases. Infect Genet Evol (2011) 0.77
In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa. AIDS (2016) 0.77
Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes. BMC Evol Biol (2011) 0.76
Special Issue: Mathematical and Computational Evolutionary Biology-2015. Syst Biol (2017) 0.75
FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets. BMC Bioinformatics (2014) 0.75
Bioinformatics of African Pathogens and Vectors conference. Editorial. Infect Genet Evol (2008) 0.75