Published in Bioinformatics on August 01, 2001
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol (2012) 40.23
Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68
Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol (2006) 14.53
Establishment of multiple sublineages of H5N1 influenza virus in Asia: implications for pandemic control. Proc Natl Acad Sci U S A (2006) 9.26
Bayesian inference of species trees from multilocus data. Mol Biol Evol (2009) 8.48
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res (2005) 8.20
The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07
How clonal is Staphylococcus aureus? J Bacteriol (2003) 7.97
Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology (2010) 7.24
Episodic radiations in the fly tree of life. Proc Natl Acad Sci U S A (2011) 7.03
Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. J Mol Evol (2005) 7.00
Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res (2006) 6.59
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics (2010) 5.70
Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet (2009) 5.37
Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature (2010) 5.22
The Amphimedon queenslandica genome and the evolution of animal complexity. Nature (2010) 5.11
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature (2008) 5.05
Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med (2008) 4.76
Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol (2013) 4.62
Mechanisms of GII.4 norovirus persistence in human populations. PLoS Med (2008) 4.57
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A (2007) 4.47
High-resolution species trees without concatenation. Proc Natl Acad Sci U S A (2007) 4.44
Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A (2005) 4.37
The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A (2003) 4.36
Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes. Proc Natl Acad Sci U S A (2006) 4.32
Phylogeny and diversification of the largest avian radiation. Proc Natl Acad Sci U S A (2004) 4.24
Phylogenetic classification of Cordyceps and the clavicipitaceous fungi. Stud Mycol (2007) 4.00
The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci U S A (2003) 3.81
Philopatry and migration of Pacific white sharks. Proc Biol Sci (2009) 3.73
Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev (2004) 3.67
Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics (2005) 3.62
Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet (2011) 3.52
topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res (2004) 3.50
Multilocus sequence typing system for the endosymbiont Wolbachia pipientis. Appl Environ Microbiol (2006) 3.45
Bayesian random local clocks, or one rate to rule them all. BMC Biol (2010) 3.44
The evolution of fungus-growing termites and their mutualistic fungal symbionts. Proc Natl Acad Sci U S A (2002) 3.43
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol (2013) 3.41
Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Lancet (2013) 3.40
LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol Bioinform Online (2007) 3.40
Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates. J Virol (2010) 3.18
Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res (2005) 3.18
Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol (2005) 3.14
Membrane lipids of symbiotic algae are diagnostic of sensitivity to thermal bleaching in corals. Proc Natl Acad Sci U S A (2004) 3.13
The genesis and evolution of H9N2 influenza viruses in poultry from southern China, 2000 to 2005. J Virol (2007) 3.12
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol (2007) 3.09
Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1). Emerg Infect Dis (2008) 3.06
Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone. Nature (2015) 3.04
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One (2009) 3.03
Single-copy nuclear genes resolve the phylogeny of the holometabolous insects. BMC Biol (2009) 2.99
New insights into myosin evolution and classification. Proc Natl Acad Sci U S A (2006) 2.97
A new time-scale for ray-finned fish evolution. Proc Biol Sci (2007) 2.92
SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics (2006) 2.92
Highly specialized microbial diversity in hyper-arid polar desert. Proc Natl Acad Sci U S A (2009) 2.91
Symbiosis and insect diversification: an ancient symbiont of sap-feeding insects from the bacterial phylum Bacteroidetes. Appl Environ Microbiol (2005) 2.91
Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol (2004) 2.91
Evolutionary history and the effect of biodiversity on plant productivity. Proc Natl Acad Sci U S A (2008) 2.90
Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology (2010) 2.90
The Near Eastern origin of cat domestication. Science (2007) 2.90
The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci U S A (2007) 2.89
Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci U S A (2002) 2.88
Murine noroviruses comprising a single genogroup exhibit biological diversity despite limited sequence divergence. J Virol (2007) 2.84
An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proc Natl Acad Sci U S A (2010) 2.83
Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell (2006) 2.82
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol (2012) 2.82
A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evol Biol (2013) 2.81
The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe (2012) 2.79
De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet (2010) 2.77
A reconsideration of the classification of the spider infraorder Mygalomorphae (Arachnida: Araneae) based on three nuclear genes and morphology. PLoS One (2012) 2.73
From offshore to onshore: multiple origins of shallow-water corals from deep-sea ancestors. PLoS One (2008) 2.68
Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi. BMC Genomics (2005) 2.66
A Silurian placoderm with osteichthyan-like marginal jaw bones. Nature (2013) 2.66
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol (2011) 2.66
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U S A (2002) 2.63
On the diversity of malaria parasites in African apes and the origin of Plasmodium falciparum from Bonobos. PLoS Pathog (2010) 2.60
Bees diversified in the age of eudicots. Proc Biol Sci (2013) 2.59
A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol Biol (2011) 2.56
Alternaria redefined. Stud Mycol (2013) 2.56
Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J Bacteriol (2003) 2.54
Viral shape-shifting: norovirus evasion of the human immune system. Nat Rev Microbiol (2010) 2.53
Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. MBio (2014) 2.50
Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol (2006) 2.48
Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol (2005) 2.48
Evolution and molecular epidemiology of H9N2 influenza A viruses from quail in southern China, 2000 to 2005. J Virol (2006) 2.47
Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci U S A (2006) 2.47
Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proc Natl Acad Sci U S A (2004) 2.46
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol (2012) 2.45
The early diversification of influenza A/H1N1pdm. PLoS Curr (2009) 2.44
Phylogenetic identification of lateral genetic transfer events. BMC Evol Biol (2006) 2.43
Multiple overseas dispersal in amphibians. Proc Biol Sci (2003) 2.43
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res (2006) 2.42
Persistent host markers in pandemic and H5N1 influenza viruses. J Virol (2007) 2.42
Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biol (2004) 2.39
Diversity and evolution of coral fluorescent proteins. PLoS One (2008) 2.36
Ancient deuterostome origins of vertebrate brain signalling centres. Nature (2012) 2.36
Complex regulation of the TIR1/AFB family of auxin receptors. Proc Natl Acad Sci U S A (2009) 2.36
Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol Biol (2009) 2.35
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res (2008) 2.35
FLOWERING LOCUS T protein may act as the long-distance florigenic signal in the cucurbits. Plant Cell (2007) 2.35
The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions. Genome Res (2009) 2.35
Bayesian inference of phylogeny and its impact on evolutionary biology. Science (2001) 11.15
Accommodating phylogenetic uncertainty in evolutionary studies. Science (2000) 2.25
Free amino Acid composition of leaf exudates and Phloem sap : a comparative study in oats and barley. Plant Physiol (1990) 1.90
The shifting roles of dispersal and vicariance in biogeography. Proc Biol Sci (2000) 1.04