Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles (Q33740739)

29 July 2017

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles (English)

1 reference

29 July 2017

2

Hervé Philippe

1 reference

29 July 2017

Nicolas Rodrigue

1

1 reference

PubMed ID

20176949

29 July 2017

Nicolas Lartillot

series ordinal

3

1 reference

PubMed ID

20176949

29 July 2017

language of work or name

English

0 references

publication date

22 February 2010

1 reference

Proceedings of the National Academy of Sciences of the United States of America

29 July 2017

1 reference

29 July 2017

107

1 reference

29 July 2017

10

1 reference

29 July 2017

4629-4634

1 reference

Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Learning to count: robust estimates for labeled distances between molecular sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Models of coding sequence evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Investigating protein-coding sequence evolution with probabilistic codon substitution models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Bayesian analysis of amino acid substitution models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Bayesian comparisons of codon substitution models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Quantifying the impact of protein tertiary structure on molecular evolution.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Population genetics without intraspecific data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

An empirical codon model for protein sequence evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Housekeeping genes for phylogenetic analysis of eutherian relationships

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Arrival and diversification of caviomorph rodents and platyrrhine primates in South America

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

The application of statistical physics to evolutionary biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Modeling the site-specific variation of selection patterns along lineages

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Protein evolution with dependence among codons due to tertiary structure.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

A nuclear gene for higher level phylogenetics: phosphoenolpyruvate carboxykinase tracks mesozoic-age divergences within Lepidoptera (Insecta).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

A codon-based model of nucleotide substitution for protein-coding DNA sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

A new method for calculating evolutionary substitution rates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

21 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

Empirical profile mixture models for phylogenetic reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

Independent origins of new sex-linked chromosomes in the melanica and robusta species groups of Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

Computing Bayes factors using thermodynamic integration.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

Conjugate Gibbs sampling for Bayesian phylogenetic models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

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/10.1073%2FPNAS.0910915107

Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

A combined empirical and mechanistic codon model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

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/10.1073%2FPNAS.0910915107

Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0910915107

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2842053

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20176949

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0910915107

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference

PubMed ID

20176949