Published in Nucleic Acids Res on July 01, 2006
The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects. BMC Genomics (2011) 1.14
A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis. BMC Res Notes (2009) 0.92
Comparative mitogenomics of plant bugs (Hemiptera: Miridae): identifying the AGG codon reassignments between serine and lysine. PLoS One (2014) 0.87
FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics (2011) 0.87
A thirty million year-old inherited heteroplasmy. PLoS One (2008) 0.85
The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria. BMC Evol Biol (2011) 0.81
Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism. Genome Biol Evol (2015) 0.80
Evolutionary analysis of mitogenomes from parasitic and free-living flatworms. PLoS One (2015) 0.77
Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals. PLoS One (2016) 0.75
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol (1993) 38.03
Position-based sequence weights. J Mol Biol (1994) 24.41
The Jalview Java alignment editor. Bioinformatics (2004) 21.74
GenBank: update. Nucleic Acids Res (2004) 12.28
A different genetic code in human mitochondria. Nature (1979) 6.41
Scoring residue conservation. Proteins (2002) 4.66
Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol (1994) 4.07
Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet (2001) 2.70
Parallel evolution of the genetic code in arthropod mitochondrial genomes. PLoS Biol (2006) 1.85
Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms. Proc Natl Acad Sci U S A (2000) 1.77
The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics (1998) 1.66
How mitochondria redefine the code. J Mol Evol (2001) 1.27
The origin of the genetic code: theories and their relationships, a review. Biosystems (2004) 1.26
First sequenced mitochondrial genome from the phylum Acanthocephala (Leptorhynchoides thecatus) and its phylogenetic position within Metazoa. J Mol Evol (2005) 0.91
jModelTest: phylogenetic model averaging. Mol Biol Evol (2008) 44.78
jModelTest 2: more models, new heuristics and parallel computing. Nat Methods (2012) 27.83
ProtTest: selection of best-fit models of protein evolution. Bioinformatics (2005) 19.16
RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics (2010) 9.49
ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics (2011) 8.68
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res (2010) 5.32
GARD: a genetic algorithm for recombination detection. Bioinformatics (2006) 4.88
Pharmacogenetic study of statin therapy and cholesterol reduction. JAMA (2004) 4.47
The causes and consequences of HIV evolution. Nat Rev Genet (2004) 4.34
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res (2010) 3.83
An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics (2007) 3.76
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell-cell communication. Bioessays (2012) 1.89
Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. Genetics (2004) 1.87
Parallel evolution of the genetic code in arthropod mitochondrial genomes. PLoS Biol (2006) 1.85
Initial diversification of living amphibians predated the breakup of Pangaea. Am Nat (2005) 1.72
Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution (2002) 1.62
A coalescent model of recombination hotspots. Genetics (2003) 1.60
Phylogenetic models of molecular evolution: next-generation data, fit, and performance. J Mol Evol (2013) 1.45
A comparison of phylogenetic network methods using computer simulation. PLoS One (2008) 1.40
Evolutionary biology in biodiversity science, conservation, and policy: a call to action. Evolution (2010) 1.36
Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics (2007) 1.27
MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol (2006) 1.27
Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries? Environ Microbiol (2006) 1.26
A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. Mol Biol Evol (2005) 1.26
The evolutionary value of recombination is constrained by genome modularity. PLoS Genet (2005) 1.26
The effect of recombination on the reconstruction of ancestral sequences. Genetics (2010) 1.25
Evolution of gastropod mitochondrial genome arrangements. BMC Evol Biol (2008) 1.24
Rapid cladogenesis in marine fishes revisited. Evolution (2005) 1.24
Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol Biol Evol (2006) 1.23
Coalescent simulation of intracodon recombination. Genetics (2009) 1.20
Genetic diversity and historical demography of Atlantic bigeye tuna (Thunnus obesus). Mol Phylogenet Evol (2005) 1.18
Analysing recombination in nucleotide sequences. Mol Ecol Resour (2011) 1.18
Rapid speciation and ecological divergence in the American seven-spined gobies (Gobiidae, Gobiosomatini) inferred from a molecular phylogeny. Evolution (2003) 1.17
Phylogenetic relationships among Opisthobranchia (Mollusca: Gastropoda) based on mitochondrial cox 1, trnV, and rrnL genes. Mol Phylogenet Evol (2004) 1.17
Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. Mol Phylogenet Evol (2004) 1.14
Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS One (2011) 1.11
Molecular phylogeny of euthyneura (mollusca: gastropoda). Mol Biol Evol (2003) 1.10
Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora). BMC Evol Biol (2003) 1.10
Evolution of the insulin receptor family and receptor isoform expression in vertebrates. Mol Biol Evol (2008) 1.05
Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evol Biol (2009) 1.04
Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol Phylogenet Evol (2006) 1.01
Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy. Infect Genet Evol (2007) 1.00
Using models of nucleotide evolution to build phylogenetic trees. Dev Comp Immunol (2005) 1.00
Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839). BMC Evol Biol (2008) 0.99
Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies. Mol Phylogenet Evol (2013) 0.99
Evolutionary analyses of gap junction protein families. Biochim Biophys Acta (2012) 0.99
Evolution of mouthbrooding and life-history correlates in the fighting fish genus Betta. Evolution (2004) 0.97
The complete mitochondrial genome of the nudibranch Roboastra europaea (Mollusca: Gastropoda) supports the monophyly of opisthobranchs. Mol Biol Evol (2002) 0.97
Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail. Evolution (2007) 0.97
Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evol Biol (2013) 0.96
Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei). Syst Biol (2006) 0.95
Characterization of phylogenetic networks with NetTest. BMC Bioinformatics (2010) 0.95
Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data. Gene (2008) 0.95
Phylogenetic relationships of Iberian dung beetles (Coleoptera: scarabaeinae): insights on the evolution of nesting behavior. J Mol Evol (2002) 0.94
Inverted replication of vertebrate mitochondria. Mol Biol Evol (2008) 0.93
Evolutionary and biogeographic patterns of the Badidae (Teleostei: Perciformes) inferred from mitochondrial and nuclear DNA sequence data. Mol Phylogenet Evol (2004) 0.93
Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology (2009) 0.93
The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates. BMC Genomics (2012) 0.93
Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba. J Acquir Immune Defic Syndr (2007) 0.92
Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba. AIDS (2005) 0.91
Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae. BMC Evol Biol (2011) 0.91
Patterns of cladogenesis in the venomous marine gastropod genus Conus from the Cape Verde islands. Syst Biol (2005) 0.89
Evolutionarily distinct residues in the uncoupling protein UCP1 are essential for its characteristic basal proton conductance. J Mol Biol (2006) 0.89
jmodeltest.org: selection of nucleotide substitution models on the cloud. Bioinformatics (2014) 0.89
Phylodynamics of HIV-1 from a phase-III AIDS vaccine trial in North America. Mol Biol Evol (2009) 0.87
The complete mitochondrial genome of the relict frog Leiopelma archeyi: insights into the root of the frog Tree of Life. Mitochondrial DNA (2010) 0.87
Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals. J Mol Evol (2009) 0.87
The complete mitochondrial DNA sequence of the Mekong giant catfish (Pangasianodon gigas), and the phylogenetic relationships among Siluriformes. Gene (2006) 0.87
Disease progression and evolution of the HIV-1 env gene in 24 infected infants. Infect Genet Evol (2007) 0.87
Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics (2013) 0.87
Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients. Virology (2007) 0.87
Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories. Mol Biol Evol (2014) 0.87
Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol Evol (2011) 0.86
Relative role of life-history traits and historical factors in shaping genetic population structure of sardines (Sardina pilchardus). BMC Evol Biol (2007) 0.86
Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae). BMC Evol Biol (2011) 0.86
Computational design of centralized HIV-1 genes. Curr HIV Res (2010) 0.85
Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology. Mol Phylogenet Evol (2008) 0.85
Characterization of reticulate networks based on the coalescent with recombination. Mol Biol Evol (2008) 0.84
On the phylogenetic position of a rare Iberian endemic mammal, the Pyrenean desman (Galemys pyrenaicus). Gene (2006) 0.84
The complete mitochondrial genome of Scutopus ventrolineatus (Mollusca: Chaetodermomorpha) supports the Aculifera hypothesis. BMC Evol Biol (2014) 0.83
Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. Syst Biol (2009) 0.83
Actinobacteria cyclophilins: phylogenetic relationships and description of new class- and order-specific paralogues. J Mol Evol (2006) 0.83
Antarctic fish mitochondrial genomes lack ND6 gene. J Mol Evol (2007) 0.82
Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial. AIDS Res Hum Retroviruses (2006) 0.82
Individual sequence variability and functional activities of fibrinogen-related proteins (FREPs) in the Mediterranean mussel (Mytilus galloprovincialis) suggest ancient and complex immune recognition models in invertebrates. Dev Comp Immunol (2010) 0.82
Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters. Gene (2005) 0.82
Oxidative stress, thermogenesis and evolution of uncoupling proteins. J Biol (2009) 0.82
Proving universal common ancestry with similar sequences. Trends Evol Biol (2012) 0.81
Phylogenetic relationships of discoglossid frogs (Amphibia:Anura:Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene (2004) 0.81
HIV-1 infected monozygotic twins: a tale of two outcomes. BMC Evol Biol (2011) 0.81
Signature of an early genetic bottleneck in a population of Moroccan sardines (Sardina pilchardus). Mol Phylogenet Evol (2005) 0.81
Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiations. Mol Phylogenet Evol (2006) 0.81
The evolution of the mitochondrial genetic code in arthropods revisited. Mitochondrial DNA (2012) 0.80
New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex. Mycologia (2010) 0.80