ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models (Q43476183)

23 November 2017

ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models (English)

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23 November 2017

Benjamin P. Blackburne

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23 November 2017

James E Allen

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David Talavera

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David Talavera

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4

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author name string

Simon Whelan

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23 November 2017

9 September 2014

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23 November 2017

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23 November 2017

64

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23 November 2017

1

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23 November 2017

42-55

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A new look at the statistical model identification

23 November 2017

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Assessing the state of substitution models describing noncoding RNA evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Bayesian model adequacy and choice in phylogenetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

ProtTest 3: fast selection of best-fit models of protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

jModelTest 2: more models, new heuristics and parallel computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

The Pfam protein families database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Statistical tests of models of DNA substitution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Markovian and non-Markovian protein sequence evolution: aggregated Markov process models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

An empirical codon model for protein sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

An improved general amino acid replacement matrix

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: evidence from case studies in the Metazoa

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

The interface of protein structure, protein biophysics, and molecular evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Performance-based selection of likelihood models for phylogeny estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

jModelTest: phylogenetic model averaging

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Selecting the Best-Fit Model of Nucleotide Substitution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Protein evolution with dependence among codons due to tertiary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

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/10.1093%2FSYSBIO%2FSYU062

Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Bayesian selection of continuous-time Markov chain evolutionary models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Model Selection in Phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Combining protein evolution and secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

The genetic code can cause systematic bias in simple phylogenetic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Estimating the frequency of events that cause multiple-nucleotide changes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Pandit: a database of protein and associated nucleotide domains with inferred trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Molecular phylogenetics: principles and practice

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

Models of amino acid substitution and applications to mitochondrial protein evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

PAML 4: phylogenetic analysis by maximum likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

A novel use of equilibrium frequencies in models of sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU062

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYU062

1 reference

23 November 2017

1 reference

PubMed ID

25209223