(Q34310772)

1 August 2017

title

Assessment of substitution model adequacy using frequentist and Bayesian methods (English)

1 reference

1 August 2017

Jennifer Ripplinger

1

1 reference

1 August 2017

Jack Sullivan

series ordinal

2

1 reference

1 August 2017

language of work or name

1 reference

8 July 2010

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Molecular Biology and Evolution

1 August 2017

published in

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1 August 2017

volume

27

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1 August 2017

issue

12

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1 August 2017

page(s)

2790-2803

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Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests

1 August 2017

cites work

1 reference

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Recovering evolutionary trees under a more realistic model of sequence evolution

6 July 2018

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The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Model use in phylogenetics: nine key questions.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Evolutionary history of the greater white-toothed shrew (Crocidura russula) inferred from analysis of mtDNA, Y, and X chromosome markers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Modeling compositional heterogeneity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

MrBayes 3: Bayesian phylogenetic inference under mixed models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Bayesian inference of phylogeny and its impact on evolutionary biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Molecular phylogenetics: state-of-the-art methods for looking into the past

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

MODELTEST: testing the model of DNA substitution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Modeling the covarion hypothesis of nucleotide substitution.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Evolution of the mitochondrial cytochrome oxidase II gene in collembola

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Success of maximum likelihood phylogeny inference in the four-taxon case

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Evolutionary trees from DNA sequences: A maximum likelihood approach

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Estimation of evolutionary distances between homologous nucleotide sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981515

Bayesian model adequacy and choice in phylogenetics.

6 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Statistical tests of models of DNA substitution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Accommodating phylogenetic uncertainty in evolutionary studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

The importance of proper model assumption in bayesian phylogenetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Performance-based selection of likelihood models for phylogeny estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Does choice in model selection affect maximum likelihood analysis?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Bayesianly Justifiable and Relevant Frequency Calculations for the Applied Statistician

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Parametric phylogenetics?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

A Stochastic Model for the Evolution of Autocorrelated DNA Sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Estimating the Dimension of a Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Model Selection in Phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Accounting for Uncertainty in the Tree Topology Has Little Effect on the Decision-Theoretic Approach to Model Selection in Phylogeny Estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSQ168

Testing a covariotide model of DNA substitution

21 January 2018

1 reference

12 December 2020

Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?

1 reference

12 December 2020

Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation

1 reference

12 December 2020

A tenth crucial question regarding model use in phylogenetics

1 reference

12 December 2020

FACTORS DETERMINING THE ACCURACY OF CLADOGRAM ESTIMATION: EVALUATION USING COMPUTER SIMULATION

1 reference

12 December 2020

Identifiers

DOI

10.1093/MOLBEV/MSQ168

1 reference

1 August 2017

1 reference

1 August 2017

1 reference