ADAPTSITE: detecting natural selection at single amino acid sites

No abstract is available for this paper.

• Publication year

  2001

• Venue

  Bioinform.

• Publication date

  2001-07-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/BIOINFORMATICS/17.7.660PMID 11448887
• 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.

• Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods

  2009cited by this paper
• Molecular evolution of pathogenic viruses

  2000cited by this paper
• A method for detecting positive selection at single amino acid sites.

  1999influential reference
• Positive Darwinian selection after gene duplication in primate ribonuclease genes.

  1998cited by this paper
• Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection.

  1989cited by this paper
• Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection

  1988cited by this paper
• MINIMUM MUTATION FITS TO A GIVEN TREE

  1973cited by this paper

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

  2025cites this paper
• Assessment of positive selection across SARS-CoV-2 variants via maximum likelihood

  2023cites this paper
• Software for Characterizing the Antigenic and Genetic Evolution of Human Influenza Viruses.

  2018cites this paper
• Conserved secondary structures predicted within the 5′ packaging signal region of influenza A virus PB2 segment

  2018cites this paper
• Complex Evolutionary History of the Mammalian Histone H1.1–H1.5 Gene Family

  2017influential citation
• Molecular Function Analysis of Rabies Virus RNA Polymerase L Protein by Using an L Gene-Deficient Virus

  2017influential citation
• Exaptation of Bornavirus-Like Nucleoprotein Elements in Afrotherians

  2016cites this paper
• Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production

  2016cites this paper
• Marine metagenomics as a source for bioprospecting.

  2015cites this paper
• Genetic characterization of porcine epidemic diarrhea virus in Korea from 1998 to 2013

  2015cites this paper
• Infectious disease informatics

  2014cites this paper
• Molecular characterization of caprine KRTAP13-3 in Liaoning cashmere goat in China

  2014cites this paper
• Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.

  2014influential citation
• Molecular Evolution of α-Latrotoxin, the Exceptionally Potent Vertebrate Neurotoxin in Black Widow Spider Venom

  2013influential citation
• Genetic diversity and molecular epidemiology of HIV transmission

  2012cites this paper
• Assessing adaptive genetic variation in cork oak expressed genes

  2012cites this paper
• Synthesis of Experimental Molecular Biology and Evolutionary Biology: An Example from the World of Vision

  2012influential citation
• Evolution of the gene translation machinery and its applications to drug discovery

  2012cites this paper
• Evaluating the Performance of Computational Approaches for Identifying Critical Sites in Protein-coding DNA Sequences

  2012cites this paper
• Isolation, recombinant expression and characterization of polymorphism of BM86 vaccine antigens homologues from Rhipicephalus Appendiculatus

  2011cites this paper
• Molecular convergence of infrared vision in snakes.

  2011cites this paper
• Analysis of recombination and natural selection in human enterovirus 71.

  2010cites this paper
• Understanding infectious agents from an in silico perspective

  2010cites this paper
• Statistical analysis of natural selection in RNA virus populations

  2010cites this paper
• Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

  2009cites this paper
• Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level.

  2009cites this paper
• The Phylogenetic Handbook: Estimating selection pressures on alignments of coding sequences

  2009cites this paper
• Genotype–phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate

  2009cites this paper
• Evolutionary replacement of UV vision by violet vision in fish

  2009cites this paper
• Methods for Analyzing Viral Evolution

  2008cites this paper
• Models of coding sequence evolution

  2008cites this paper
• DETECTING MOLECULAR EVIDENCE OF POSITIVE DARWINIAN SELECTION

  2008cites this paper
• Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

  2008cites this paper
• Comparative and evolutionary genomics of globin genes in fish.

  2008cites this paper
• Nitric oxide synthase (NOS) in the Japanese fireflies Luciola lateralis and Luciola cruciata.

  2008cites this paper
• Comparative Studies of RNA Virus Evolution

  2008cites this paper
• etecting recombination and diversifying selection in human lpha-papillomavirus

  2008cites this paper
• WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding

  2008cites this paper
• Detecting recombination and diversifying selection in human alpha-papillomavirus.

  2008cites this paper
• Author ' s personal copy Approaches for identifying targets of positive selection

  2007cites this paper
• BoLA class I allele diversity and polymorphism in a herd of cattle

  2007cites this paper
• Genomic and microarray approaches to coral reef conservation biology

  2007cites this paper
• Structural and functional implications of positive selection at the primate angiogenin gene

  2007cites this paper
• The Evolution of the Hh-Signaling Pathway Genes: A Computer-Assisted Study

  2007cites this paper
• Estimating selection pressures on alignments of coding sequences Analyses using HyPhy

  2007cites this paper
• Genetic Stability of Human T Lymphotropic Virus Type I despite Antiviral Pressures by CTLs1

  2007cites this paper
• Approaches for identifying targets of positive selection.

  2007cites this paper
• specialization, and efficient decoding for translation optimization Codon usage bias from tRNA's point of view: Redundancy,

  2007cites this paper
• New methods for inferring population dynamics from microbial sequences.

  2007cites this paper
• Study of Swine Leukocyte Antigen Class I-3 (SLA-3) Gene for Inbreeding Wuzhishan Pig

  2007cites this paper
• Inferring natural selection operating on conservative and radical substitution at single amino acid sites.

  2007cites this paper
• Detection of positive selection resulting from Nevirapine treatment in longitudinal HIV-1 reverse transcriptase sequences

  2006cites this paper
• Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes

  2006cites this paper
• Comparisons of dN/dS are time dependent for closely related bacterial genomes.

  2006cites this paper
• Natural selection on the influenza virus genome.

  2006cites this paper
• Statistical properties of the methods for detecting positively selected amino acid sites.

  2006influential citation
• Natural Selection on the Influenza Virus Genome

  2006influential citation
• Analytical methods for studying the evolution of paralogs using duplicate gene datasets.

  2005influential citation
• Datamonkey: rapid detection of selective pressure on individual sites of codon alignments

  2005cites this paper
• Large‐scale prediction of function shift in protein families with a focus on enzymatic function

  2005cites this paper
• Interchromosomal segmental duplications explain the unusual structure of PRSS3, the gene for an inhibitor-resistant trypsinogen.

  2005cites this paper
• The Origin and Evolution of Porcine Reproductive and Respiratory Syndrome Viruses

  2005cites this paper
• Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates.

  2005cites this paper
• Multilocus Sequence Typing of Streptococcus uberis Provides Sensitive and Epidemiologically Relevant Subtype Information and Reveals Positive Selection in the Virulence Gene pauA

  2005cites this paper
• Predicting enzyme function from protein sequence.

  2005cites this paper
• Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization.

  2004cites this paper
• Negative selection on neutralization epitopes of poliovirus surface proteins: implications for prediction of candidate epitopes for immunization.

  2004influential citation
• New Methods for Detecting Positive Selection at Single Amino Acid Sites

  2004cites this paper
• Strong Positive Selection and Recombination Drive the Antigenic Variation of the PilE Protein of the Human Pathogen Neisseria meningitidis

  2004cites this paper
• Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites

  2004influential citation
• Three-dimensional window analysis for detecting positive selection at structural regions of proteins.

  2004influential citation
• Differential selection of genes of cucumber mosaic virus subgroups.

  2004influential citation
• False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus.

  2004influential citation
• Power in numbers : in silico analysis of multigene families in Arabidopsis thaliana

  2003cites this paper
• The effect of positive selection on a sexual reproduction gene in Thalassiosira weissflogii (Bacillariophyta): results obtained from maximum-likelihood and parsimony-based methods.

  2003influential citation
• Genetic polymorphism of the swine major histocompatibility complex (SLA) class I genes, SLA-1, -2 and -3

  2003cites this paper
• Bayesian Methods for Phylogeny Independent Detection of Positively Selected Amino Acid Sites

  2003cites this paper
• Interpretive proteomics--finding biological meaning in genome and proteome databases.

  2003influential citation
• Current Awareness on Comparative and Functional Genomics

  2002cites this paper
• HIV subtype C diversity: analysis of the relationship of sequence diversity to proposed epitope locations

  2002cites this paper
• Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone

  2002cites this paper
• Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites.

  2002cites this paper
• A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins

  2001cites this paper
• Comparison of Bayesian , maximum likelihood and parsimony methods for detecting positive selection ( Research Article )

  year unknowncites this paper