(Q40264737)

19 September 2017

Bayesian selection of nucleotide substitution models and their site assignments (English)

1 reference

19 September 2017

3

1 reference

19 September 2017

Chieh-Hsi Wu

1

0 references

Marc A. Suchard

series ordinal

2

object named as

Marc A Suchard

1 reference

19 September 2017

11 December 2012

1 reference

Molecular Biology and Evolution

19 September 2017

1 reference

19 September 2017

30

1 reference

19 September 2017

3

1 reference

19 September 2017

669-688

1 reference

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

19 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Purifying selection can obscure the ancient age of viral lineages

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

The mode and tempo of hepatitis C virus evolution within and among hosts

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Among-site rate variation and its impact on phylogenetic analyses

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Bayesian inference of species trees from multilocus data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Bayesian phylogeography finds its roots

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Bayesian analysis of amino acid substitution models

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Relaxed phylogenetics and dating with confidence

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Joint Bayesian Estimation of Alignment and Phylogeny

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G protein

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Bayesian coalescent inference of past population dynamics from molecular sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Hierarchical Phylogenetic Models for Analyzing Multipartite Sequence Data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Using evolutionary methods to study G-protein coupled receptors.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

The epidemic behavior of the hepatitis C virus

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Bayesian selection of continuous-time Markov chain evolutionary models

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Genetic epidemiology of hepatitis C virus throughout egypt

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

MODELTEST: testing the model of DNA substitution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Variation in the pattern of nucleotide substitution across sites

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Genealogical inference from microsatellite data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Assessing the impact of secondary structure and solvent accessibility on protein evolution.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Evolutionary trees from DNA sequences: A maximum likelihood approach

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Sample size for a phylogenetic inference

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Empirical profile mixture models for phylogenetic reconstruction

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

A nonparametric method for accommodating and testing across-site rate variation

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Bayesian phylogenetic inference via Markov chain Monte Carlo methods.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Using protein structural information in evolutionary inference: transmembrane proteins

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563969

Reversible jump Markov chain Monte Carlo computation and Bayesian model determination

20 August 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS258

Monte Carlo sampling methods using Markov chains and their applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS258

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS258

Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS258

Model Selection in Phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS258

A Bayesian Analysis of Some Nonparametric Problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS258

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%2FMSS258

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites

21 January 2018

1 reference

12 December 2020

Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes

1 reference

12 December 2020

General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites

1 reference

12 December 2020

Estimates of DNA and protein sequence divergence: an examination of some assumptions

1 reference

12 December 2020

Limitations of the evolutionary parsimony method of phylogenetic analysis

1 reference

12 December 2020

Spatial and temporal heterogeneity in nucleotide sequence evolution

1 reference

12 December 2020

Modeling evolution at the protein level using an adjustable amino acid fitness model

1 reference

12 December 2020

Modeling residue usage in aligned protein sequences via maximum likelihood

1 reference

12 December 2020

Identifiers

DOI

10.1093/MOLBEV/MSS258

1 reference

19 September 2017

1 reference

19 September 2017

1 reference

PMCID

3563969