A random effects branch-site model for detecting episodic diversifying selection. (Q35639190)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21670087%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

title

A random effects branch-site model for detecting episodic diversifying selection (English)

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4 February 2020

2

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4 February 2020

Mathieu Fourment

3

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4 February 2020

Simon Frost

4

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4 February 2020

Konrad Scheffler

6

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Sergei L. Kosakovsky Pond

4 February 2020

1

object named as

Sergei L Kosakovsky Pond

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4 February 2020

author name string

Wayne Delport

5

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4 February 2020

publication date

13 June 2011

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Molecular Biology and Evolution

4 February 2020

published in

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4 February 2020

volume

28

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4 February 2020

issue

11

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4 February 2020

page(s)

3033-3043

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Correcting the bias of empirical frequency parameter estimators in codon models

4 February 2020

cites work

1 reference

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

27 July 2018

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Evolutionary fingerprinting of genes.

27 July 2018

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Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

27 July 2018

1 reference

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Frequent toggling between alternative amino acids is driven by selection in HIV-1

27 July 2018

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Models of coding sequence evolution

27 July 2018

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A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus.

27 July 2018

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Site-to-site variation of synonymous substitution rates

27 July 2018

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A genomics approach to the detection of positive selection in cattle: adaptive evolution of the T-cell and natural killer cell-surface protein CD2.

27 July 2018

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

27 July 2018

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Bayes empirical bayes inference of amino acid sites under positive selection

27 July 2018

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

27 July 2018

1 reference

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HyPhy: hypothesis testing using phylogenies

27 July 2018

1 reference

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Modeling the site-specific variation of selection patterns along lineages

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

Episodic adaptive evolution of primate lysozymes.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

A Hidden Markov Model approach to variation among sites in rate of evolution

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

CodonTest: modeling amino acid substitution preferences in coding sequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

Investigating protein-coding sequence evolution with probabilistic codon substitution models

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

Detecting amino acid sites under positive selection and purifying selection

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

A genetic algorithm approach to detecting lineage-specific variation in selection pressure.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3247808

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

25 September 2018

1 reference

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

25 September 2018

1 reference

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

25 September 2018

1 reference

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

25 September 2018

1 reference

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Evolutionary trees from DNA sequences: A maximum likelihood approach

25 September 2018

1 reference

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A method for detecting positive selection at single amino acid sites

25 September 2018

1 reference

12 December 2020

Statistical properties of the branch-site test of positive selection

1 reference

12 December 2020

Frequent false detection of positive selection by the likelihood method with branch-site models

1 reference

12 December 2020

Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites

1 reference

12 December 2020

Identifiers

DOI

10.1093/MOLBEV/MSR125

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21670087%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21670087%20AND%20SRC:MED&resulttype=core&format=json

4 February 2020

1 reference