Investigating protein-coding sequence evolution with probabilistic codon substitution models (Q37298963)

19 August 2017

title

Investigating protein-coding sequence evolution with probabilistic codon substitution models (English)

1 reference

19 August 2017

main subject

probabilistic modeling

0 references

0 references

Maria Anisimova

1 reference

19 August 2017

Carolin Kosiol

series ordinal

1 reference

19 August 2017

publication date

14 October 2008

1 reference

Molecular Biology and Evolution

19 August 2017

published in

1 reference

19 August 2017

1 reference

19 August 2017

1 reference

19 August 2017

page(s)

255-271

1 reference

Gene conversion and functional divergence in the beta-globin gene family

19 August 2017

cites work

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Translational selection and molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Phylogenomic analysis of natural selection pressure in Streptococcus genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Accuracy and power of bayes prediction of amino acid sites under positive selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

The quest for natural selection in the age of comparative genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Positive and negative selection in the beta-esterase gene cluster of the Drosophila melanogaster subgroup.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Amino acid substitution during functionally constrained divergent evolution of protein sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Maximum likelihood methods for detecting adaptive evolution after gene duplication.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A site- and time-heterogeneous model of amino acid replacement.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Variation in evolutionary processes at different codon positions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

SIMMAP: stochastic character mapping of discrete traits on phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Disease progression and evolution of the HIV-1 env gene in 24 infected infants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Hearing silence: non-neutral evolution at synonymous sites in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Ancestral gene reconstruction and synthesis of ancient rhodopsins in the laboratory

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Quantifying the impact of protein tertiary structure on molecular evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Rhodopsin evolution in the dark

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Detecting coevolving amino acid sites using Bayesian mutational mapping

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A combined empirical and mechanistic codon model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Relaxed phylogenetics and dating with confidence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

BEAST: Bayesian evolutionary analysis by sampling trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evolution of synonymous codon usage in metazoans

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Rate of change of concomitantly variable codons

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A codon-based model of host-specific selection in parasites, with an application to the influenza A virus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A nonhyperthermophilic common ancestor to extant life forms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Statistical tests of models of DNA substitution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Darwin v. 2.0: an interpreted computer language for the biosciences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Amino acid difference formula to help explain protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Modeling the site-specific variation of selection patterns along lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Simulating DNA coding sequence evolution with EvolveAGene 3.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Monte Carlo sampling methods using Markov chains and their applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Neuroendocrine immunity in patients with Alzheimer's disease: toward translational epigenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

CpG + CpNpG analysis of protein-coding sequences from tomato

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

An expectation maximization algorithm for training hidden substitution models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Bayesian estimation of positively selected sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

MRBAYES: Bayesian inference of phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Reconstruction of ancestral FGLamide-type insect allatostatins: a novel approach to the study of allatostatin function and evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Modeling the impact of DNA methylation on the evolution of BRCA1 in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

RETRACTED: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A "silent" polymorphism in the MDR1 gene changes substrate specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Performance of a divergence time estimation method under a probabilistic model of rate evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

XRate: a fast prototyping, training and annotation tool for phylo-grammars

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Genetics. SNPs, silent but not invisible.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Not so different after all: a comparison of methods for detecting amino acid sites under selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Adaptation to different human populations by HIV-1 revealed by codon-based analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

HyPhy: hypothesis testing using phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Site-to-site variation of synonymous substitution rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Estimating selection pressures on HIV-1 using phylogenetic likelihood models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

GARD: a genetic algorithm for recombination detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Automated phylogenetic detection of recombination using a genetic algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Mutation matrices and physical-chemical properties: correlations and implications

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A new criterion and method for amino acid classification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

An empirical codon model for protein sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Patterns of positive selection in six Mammalian genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Computing Bayes factors using thermodynamic integration.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evolutionary dynamics of human retroviruses investigated through full-genome scanning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

An algorithm for progressive multiple alignment of sequences with insertions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Detecting amino acid sites under positive selection and purifying selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A gamma mixture model better accounts for among site rate heterogeneity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

The evolution of codon preferences in Drosophila: a maximum-likelihood approach to parameter estimation and hypothesis testing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Episodic adaptive evolution of primate lysozymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Performance-based selection of likelihood models for phylogeny estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A scan for positively selected genes in the genomes of humans and chimpanzees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A codon-based model designed to describe lentiviral evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

MODELTEST: testing the model of DNA substitution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Inferring speciation times under an episodic molecular clock

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

An empirical examination of the utility of codon-substitution models in phylogeny reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evolutionary models for insertions and deletions in a probabilistic modeling framework

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Protein evolution with dependence among codons due to tertiary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Assessing site-interdependent phylogenetic models of sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

MrBayes 3: Bayesian phylogenetic inference under mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Robust inference of positive selection from recombining coding sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A Bayesian Model Comparison Approach to Inferring Positive Selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Empirical codon substitution matrix

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

A model of directional selection applied to the evolution of drug resistance in HIV-1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Combining phylogenetic and hidden Markov models in biosequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

An Evolutionary Space-Time Model with Varying Among-Site Dependencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Population genetics without intraspecific data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evolution of coral pigments recreated.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Bayesian Model Selection and Model Averaging

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Estimating the frequency of events that cause multiple-nucleotide changes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Estimating diversifying selection and functional constraint in the presence of recombination

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Identification of physicochemical selective pressure on protein encoding nucleotide sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

The 'effective number of codons' used in a gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

PAML 4: phylogenetic analysis by maximum likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Statistical methods for detecting molecular adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Bayes empirical bayes inference of amino acid sites under positive selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Transducers: an emerging probabilistic framework for modeling indels on trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Positive selection at sites of multiple amino acid replacements since rat–mouse divergence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

Evolutionary nucleotide replacements in DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSN232

21 January 2018

Identifiers

DOI

10.1093/MOLBEV/MSN232

1 reference

release_x4ic3gpzezaktpumx74rrcvvbi

19 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/x4ic3gpzezaktpumx74rrcvvbi

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference