Codon-substitution models for heterogeneous selection pressure at amino acid sites.

No abstract is available for this paper.

• Publication year

  2000

• Venue

  Genetics

• Publication date

  2000-04-29

• Fields of study

  Biology, Mathematics, Medicine

• Identifiers
  PMID 10790415PMCID PMC1461088
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Evolutionary trees from DNA sequences: A maximum likelihood approach

  2005cited by this paper
• Coalescing into the 21st century: An overview and prospects of coalescent theory.

  1999cited by this paper
• Within- and between-species DNA sequence variation and the 'footprint' of natural selection.

  1999cited by this paper
• Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection.

  1999cited by this paper
• Genealogical evidence for positive selection in the nef gene of HIV-1.

  1999cited by this paper
• Statistical tests of neutrality in the age of weak selection.

  1998cited by this paper
• Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders

  1998cited by this paper
• HIV-1 regulatory/accessory genes: keys to unraveling viral and host cell biology.

  1998cited by this paper
• Tempo and Mode of Nucleotide Substitution in gag andenv Gene Fragments in Human Immunodeficiency Virus Type 1 Populations with a Known Transmission History

  1998cited by this paper
• Models of molecular evolution and phylogeny.

  1998cited by this paper
• Phylogeny of the Genus Flavivirus

  1998cited by this paper
• A codon-based model designed to describe lentiviral evolution.

  1998cited by this paper
• Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene.

  1998cited by this paper
• Episodic adaptive evolution of primate lysozymes

  1997cited by this paper
• In search of molecular darwinism

  1997cited by this paper
• PAML: a program package for phylogenetic analysis by maximum likelihood

  1997cited by this paper
• Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts.

  1997cited by this paper
• Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history

  1997cited by this paper
• Long term trends in the evolution of H(3) HA1 human influenza type A.

  1997cited by this paper
• The ratio of replacement to silent divergence and tests of neutrality

  1997cited by this paper
• Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees.

  1996cited by this paper
• Large-scale search for genes on which positive selection may operate.

  1996cited by this paper
• Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates.

  1996cited by this paper
• Population dynamics of flaviviruses revealed by molecular phylogenies.

  1996cited by this paper
• Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1).

  1995cited by this paper
• The molecular epidemiology of human immunodeficiency virus type 1 in Edinburgh.

  1995cited by this paper
• Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.

  1995cited by this paper
• A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.

  1994cited by this paper
• A codon-based model of nucleotide substitution for protein-coding DNA sequences.

  1994cited by this paper
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

  1994cited by this paper
• Statistical tests of models of DNA substitution

  1993cited by this paper
• THE NEARLY NEUTRAL THEORY OF MOLECULAR EVOLUTION

  1992influential reference
• Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection

  1988cited by this paper
• Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests under Nonstandard Conditions

  1987cited by this paper
• A test of neutral molecular evolution based on nucleotide data.

  1987cited by this paper
• Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.

  1986cited by this paper
• The neutral theory of molecular evolution.

  1983influential reference
• The neutral theory of molecular evolution

  1983cited by this paper
• Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application

  1980cited by this paper
• A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

  1980cited by this paper
• A new look at the statistical model identification

  1974cited by this paper
• The Incomplete Gamma Integral

  1970cited by this paper
• Molecular Evolution

  year unknowncited by this paper
• A Maximum-likelihood Approach

  year unknowncited by this paper

• Comparative Mitogenomics and Phylogeny of Geotrupidae (Insecta: Coleoptera): Insights from Two New Mitogenomes of Qinghai–Tibetan Plateau Dung Beetles

  2026cites this paper
• Coevolution Between Three-Finger Toxins and Target Receptors

  2026cites this paper
• Genomic basis of the evolution of vertical bars in clownfishes

  2026cites this paper
• Natural selection on synonymous genetic variation in the major histocompatibility complex

  2026cites this paper
• PKN is a sex- and species-specific fertilization factor in brown algae

  2026cites this paper
• Gene loss and positively selected genes in chloroplast genomes reveal adaptive evolution in Styracaceae

  2026cites this paper
• New Insights Into the Evolution of Immune Adaptors in Murid Rodents

  2026cites this paper
• Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution

  2025cites this paper
• Mitogenomics of endemic Ethiopian shrews: looking for footprints of adaptive evolution along a remarkable altitudinal gradient

  2025cites this paper
• Comparative chloroplast genomes and phylogenetic analysis of the Phlegmariurus (Lycopodiaceae) from China and neighboring regions

  2025cites this paper
• Female membrane proteins regulate postmating ovulation in Drosophila melanogaster by ovulin-dependent and -independent pathways

  2025cites this paper
• Multiple Retrotransposon-mediated NF-YA Gene Duplication Events Recurred in Diverse Groups of Mammals at Different Ancestry Levels

  2025cites this paper
• Detecting signatures of episodic positive selection based on observed amino acids in hemagglutinin of H3N2 human influenza A virus

  2025cites this paper
• ASR gene family: a case of tandem-drive evolution

  2025cites this paper
• Trends in substitution models of protein evolution for phylogenetic inference.

  2025cites this paper
• Evolution of canonical circadian clock genes underlies unique sleep strategies of marine mammals for secondary aquatic adaptation

  2025cites this paper
• Molecular Evolution of the Green-Sensitive Opsins (RH2) in Sulawesi Oryzias Species with a Single Origin

  2025cites this paper
• Genome-wide comprehensive analysis the molecular phylogenetic evolution, functional divergence and tissue-specific expression of GH3 gene family in Salvia miltiorrhiza, Arabidopsis thaliana, and Oryza sativa

  2025influential citation
• Machine Learning‐Enhanced Random Matrix Theory Design for Human Immunodeficiency Virus Vaccine Development

  2025cites this paper
• Molecular evolution of octopamine receptors in Drosophila

  2025cites this paper
• The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire

  2025cites this paper
• Novel Reoviruses of Waterfowl Origin in Northern Vietnam: A Laboratory Investigation

  2025cites this paper
• Unveiling hidden parasite diversity: Long-read mitogenomics in Eimeriidae and Haemosporida (Eukaryota: Apicomplexa).

  2025cites this paper
• An orphan gene is essential for efficient sperm entry into eggs in Drosophila melanogaster.

  2025cites this paper
• Deciphering genetic adaptations of Old World camels through comparative genomic analyses across all camelid species

  2025cites this paper
• Genetic basis of the evolution of vertical bars in clownfishes

  2025cites this paper
• Molecular and epidemiological analysis of measles vaccine-associated rash illnesses in Shandong province, China, 2014–2021.

  2025cites this paper
• An evolutionary dynamics analysis of the plant DEK gene family reveals the role of BnaA02g08940D in drought tolerance.

  2025cites this paper
• Heterogeneous Evolution Among SARS‐CoV‐2 Genes and Variants of Concern

  2025cites this paper
• Applying the Classic Test dN/dS to Detect Selection in Archaea.

  2025cites this paper
• Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids

  2025cites this paper
• Adaptive evolution and phylogeny of cerithioid gastropods with six new mitogenomes

  2025cites this paper
• Genome-Wide Variation Profile of the Genus Tobamovirus

  2025cites this paper
• Immunogenetic diversity and haemosporidian parasitization in European bluethroats (Luscinia svecica): do diverse genes warrant fewer parasites?

  2025cites this paper
• Genomic profiles of Pyricularia oryzae in Sub-Saharan Africa: exploring population differences and their evolutionary implications in the region

  2025cites this paper
• Molecular evolution of octopamine receptors in Drosophila

  2025influential citation
• Trichromacy is insufficient for mate detection in a mimetic butterfly

  2025cites this paper
• Detecting Interspecific Positive Selection Using Convolutional Neural Networks

  2024cites this paper
• Structural Features and Phylogenetic Implications of Crinoid Echinoderms Based on Thirteen Novel Mitochondrial Genomes

  2024cites this paper
• Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid wasps

  2024cites this paper
• Advance typing of Vibrio parahaemolyticus through the mtlA and aer gene: A high-resolution, cost-effective approach

  2024influential citation
• Functional analysis of fasciclin-like arabinogalactan in carotenoid synthesis during tomato fruit ripening.

  2024cites this paper
• Many-core algorithms for high-dimensional gradients on phylogenetic trees

  2024cites this paper
• Positive selection and functional diversification of transcription factor Cmr1 homologs in Alternaria

  2024cites this paper
• Identifying Rapidly Evolving Genes in Coral Species to Better Understand Coral Bleaching

  2024cites this paper
• Insight Into Body Size Evolution in Aves: Based on Some Body Size‐Related Genes

  2024cites this paper
• Cloning, characterization, and evolutionary patterns of KCNQ4 genes in anurans

  2024cites this paper
• Positive Selection of TLR2 and MyD88 Genes Provides Insights Into the Molecular Basis of Immunological Adaptation in Amphibians

  2024cites this paper
• Adaptation in human immune cells residing in tissues at the frontline of infections

  2024influential citation
• An orphan gene is essential for efficient sperm entry into eggs in Drosophila melanogaster

  2024influential citation
• Pathogenesis related proteins: milestones in five decades of research

  2024cites this paper
• Influence of life-history traits on mitochondrial DNA substitution rates exceeds that of metabolic rates in teleost fishes

  2024cites this paper
• Mimetic butterfly wings through mimetic butterfly eyes

  2024cites this paper
• Seven mitochondrial genomes of tribe Hylurgini (Coleoptera: Curculionidae: Scolytinae) in Eurasia and their phylogenetic analysis

  2024cites this paper
• Widespread adaptive evolution in angiosperm photosystems provides insight into the evolution of photosystem II repair

  2024cites this paper
• Endemic Radiation of African Moonfish, Selene dorsalis (Gill 1863), in the Eastern Atlantic: Mitogenomic Characterization and Phylogenetic Implications of Carangids (Teleostei: Carangiformes)

  2024cites this paper
• Detection of positive selection driving antimicrobial resistance in the core genome of Staphylococcus epidermidis

  2024cites this paper
• Varying Selection Pressure for a Na+ Sensing Site in Epithelial Na+ Channel Subunits Reflect Divergent Roles in Na+ Homeostasis

  2024cites this paper
• Molecular evolution and genetic diversity of defective chorion 1 in Anastrepha fraterculus and Anastrepha obliqua (Diptera, Tephritidae)

  2024cites this paper
• CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure

  2024cites this paper
• Unlocking expanded flagellin perception through rational receptor engineering

  2024cites this paper
• Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean

  2024cites this paper
• Signals of positive selection in genomes of palearctic Myotis-bats coexisting with a fungal pathogen

  2024cites this paper
• Genetic diversity of HPV35 in Chad and the Central African Republic, two landlocked countries of Central Africa: A cross-sectional study

  2024influential citation
• Comparative genomics reveals convergent signals associated with the high metabolism and longevity in birds and bats

  2024cites this paper
• Does metabolic rate influence genome-wide amino acid composition in the course of animal evolution?

  2024cites this paper
• Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea

  2024cites this paper
• Diversity and Evolution of NLR Genes in Citrus Species

  2024cites this paper
• In silico analysis of Phaseolus vulgaris L. metalloprotease FtsH gene: characterization and expression in drought and salt stress

  2024cites this paper
• Analysis of Evolutionary Conservation, Expression Level, and Genetic Association at a Genome-wide Scale Reveals Heterogeneity Across Polygenic Phenotypes

  2024cites this paper
• From molecular variations to behavioral adaptations: Unveiling adaptive epistasis in primate oxytocin system.

  2024cites this paper
• Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs

  2024cites this paper
• Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations

  2024cites this paper
• Evolutionary characteristics of the mitochondrial NADH dehydrogenase subunit 6 gene in some populations of four sympatric Mustela species (Mustelidae, Mammalia) from central Europe

  2024cites this paper
• Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes

  2024cites this paper
• Genome-wide characterization and functional analysis of heat shock transcription factors in wild and cultivated rice (Oryza sativa L.)

  2024cites this paper
• Breathing Air and Living Underwater: Molecular Evolution of Genes Related to Antioxidant Response in Cetaceans and Pinnipeds

  2024cites this paper
• The complete mitochondrial genome of Heikeopsis japonica (Decapoda: Brachyura: Dorippidae): Phylogenetic implications of the family Dorippidae

  2024cites this paper
• Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes

  2024cites this paper
• Signals of positive selection in Palearctic bat species coexisting with a fungal pathogen

  2023cites this paper
• Convergent origin and accelerated evolu0on of 3 vesicle-associated RhoGAP proteins in two 4 unrelated parasitoid wasps 5

  2023cites this paper
• Chromosome‐level genome assembly of the aster leafhopper (Macrosteles quadrilineatus) reveals the role of environment and microbial symbiosis in shaping pest insect genome evolution

  2023influential citation
• Turtle and tortoise mitogenomes under contrasting positive selection pressure

  2023influential citation
• Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice

  2023cites this paper
• Ribonucleotide reductase as a therapeutic target for drug repurposing as anthelmintics.

  2023cites this paper
• Molecular Evolution and Protein Structure Variation of Dkk Family

  2023cites this paper
• Evolution of Three-Finger Toxin Genes in Neotropical Colubrine Snakes (Colubridae)

  2023cites this paper
• Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission

  2023cites this paper
• Evolutionary analysis of the mTOR pathway provide insights into lifespan extension across mammals

  2023cites this paper
• Pandemic preparedness through genomic surveillance: Overview of mutations in SARS-CoV-2 over the course of COVID-19 outbreak

  2023cites this paper
• Genome-wide survey and evolutionary history of the Pectin methylesterase (PME) gene family in the Dothideomycetes class of fungi.

  2023cites this paper
• Phylogeny and evolution of the SARS-CoV-2 spike gene from December 2022 to February 2023

  2023cites this paper
• Genetics and Molecular Biology

  2023cites this paper
• Generation of accurate, expandable phylogenomic trees with uDance

  2023cites this paper
• Quantifying Adaptive Evolution of the Human Immune Cell Landscape

  2023cites this paper
• Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh

  2023cites this paper
• The paradoxes of Mycobacterium tuberculosis molecular evolution and consequences for the inference of tuberculosis emergence date.

  2023cites this paper
• The influence of GC-biased gene conversion on nonadaptive sequence evolution in short introns of Drosophila melanogaster

  2023cites this paper
• Responses to predation pressure involve similar sets of genes in two divergent species of Daphnia.

  2023cites this paper
• Protein subcellular relocalization and function of duplicated flagellar calcium binding protein genes in honey bee trypanosomatid parasite

  2023cites this paper