(Q43197803)

15 November 2017

On the statistical interpretation of site-specific variables in phylogeny-based substitution models (English)

1 reference

15 November 2017

0 references

1 reference

Nicolas Rodrigue

1

1 reference

PMC publication ID

3567744

15 November 2017

language of work or name

English

0 references

publication date

5 December 2012

1 reference

15 November 2017

1 reference

15 November 2017

193

1 reference

15 November 2017

2

1 reference

15 November 2017

557-564

1 reference

Modeling HIV-1 drug resistance as episodic directional selection

15 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Fast Bayesian choice of phylogenetic models: prospecting data augmentation-based thermodynamic integration

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Among-site rate variation and its impact on phylogenetic analyses

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Charting the host adaptation of influenza viruses

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Identifying changes in selective constraints: host shifts in influenza.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Bayesian comparisons of codon substitution models

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Exploring fast computational strategies for probabilistic phylogenetic analysis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Site-to-site variation of synonymous substitution rates

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Taking variation of evolutionary rates between sites into account in inferring phylogenies

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Evolutionary trees from DNA sequences: A maximum likelihood approach

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Conjugate Gibbs sampling for Bayesian phylogenetic models.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

A gamma mixture model better accounts for among site rate heterogeneity

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

Detecting amino acid sites under positive selection and purifying selection

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567744

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

15 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23222651

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Modeling residue usage in aligned protein sequences via maximum likelihood

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23222651

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1534/GENETICS.112.145722

1 reference

15 November 2017

1 reference

PMC publication ID

3567744

15 November 2017

PubMed publication ID

23222651

1 reference

PMC publication ID

3567744