(Q33923545)

30 July 2017

title

An experimentally determined evolutionary model dramatically improves phylogenetic fit. (English)

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30 July 2017

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1

1 reference

30 July 2017

publication date

24 May 2014

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Molecular Biology and Evolution

30 July 2017

published in

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30 July 2017

volume

31

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30 July 2017

issue

8

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30 July 2017

page(s)

1956-1978

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A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data

30 July 2017

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Correcting the bias of empirical frequency parameter estimators in codon models

5 July 2018

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Permissive secondary mutations enable the evolution of influenza oseltamivir resistance

5 July 2018

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5 July 2018

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Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene

5 July 2018

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

5 July 2018

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Statistical potentials for improved structurally constrained evolutionary models.

5 July 2018

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5 July 2018

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A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

5 July 2018

1 reference

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5 July 2018

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5 July 2018

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Highly conserved regions of influenza a virus polymerase gene segments are critical for efficient viral RNA packaging.

5 July 2018

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5 July 2018

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Beneficial mutation selection balance and the effect of linkage on positive selection

5 July 2018

1 reference

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Population genetics without intraspecific data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

An empirical codon model for protein sequence evolution

5 July 2018

1 reference

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The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA

5 July 2018

1 reference

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Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein.

5 July 2018

1 reference

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Thermodynamics of neutral protein evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Protein stability promotes evolvability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Bayes empirical bayes inference of amino acid sites under positive selection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Thermodynamic prediction of protein neutrality

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

HyPhy: hypothesis testing using phylogenies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

WebLogo: A Sequence Logo Generator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Generating mutant libraries using error-prone PCR.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

The influenza virus nucleoprotein: a multifunctional RNA-binding protein pivotal to virus replication.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Bayesian inference of phylogeny and its impact on evolutionary biology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

EMBOSS: the European Molecular Biology Open Software Suite

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

A DNA transfection system for generation of influenza A virus from eight plasmids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Generation of influenza A viruses entirely from cloned cDNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

A novel mechanism for the acquisition of virulence by a human influenza A virus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Synonymous and nonsynonymous rate variation in nuclear genes of mammals.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Evolutionary trees from DNA sequences: A maximum likelihood approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Measurement of the mutation rates of animal viruses: influenza A virus and poliovirus type 1.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Sequence logos: a new way to display consensus sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters

5 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU173

Equation of State Calculations by Fast Computing Machines

21 January 2018

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU173

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU173

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU173

Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU173

Combining protein evolution and secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU173

Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104320

29 October 2018

Identifiers

DOI

10.1093/MOLBEV/MSU173

1 reference

30 July 2017

1 reference

30 July 2017

1 reference