(Q38889795)

7 September 2017

Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories (English)

1 reference

7 September 2017

1

1 reference

7 September 2017

2

1 reference

7 September 2017

19 February 2014

1 reference

Molecular Biology and Evolution

7 September 2017

1 reference

7 September 2017

31

1 reference

7 September 2017

5

1 reference

7 September 2017

1295-1301

1 reference

Protein evolution along phylogenetic histories under structurally constrained substitution models.

7 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Simulation of molecular data under diverse evolutionary scenarios

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Computer simulations: tools for population and evolutionary genetics

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

ALF--a simulation framework for genome evolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Genome-wide heterogeneity of nucleotide substitution model fit.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Evidence of positive selection at codon sites localized in extracellular domains of mammalian CC motif chemokine receptor proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Genome-wide scans for footprints of natural selection

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Coalescent simulation of intracodon recombination

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

INDELible: a flexible simulator of biological sequence evolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

GENOMEPOP: a program to simulate genomes in populations

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

jModelTest: phylogenetic model averaging

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

PAML 4: phylogenetic analysis by maximum likelihood

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

An empirical codon model for protein sequence evolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

The Stepping Stone Model of Population Structure and the Decrease of Genetic Correlation with Distance

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

EVOLUTION IN MENDELIAN POPULATIONS

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Empirical codon substitution matrix

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

ProtTest: selection of best-fit models of protein evolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

HyPhy: hypothesis testing using phylogenies

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

A coalescent model of recombination hotspots

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Generating samples under a Wright-Fisher neutral model of genetic variation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

The coalescent process in models with selection and recombination

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

The genome of murine cytomegalovirus is shaped by purifying selection and extensive recombination

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

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

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

The importance of proper model assumption in bayesian phylogenetics.

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Using protein structural information in evolutionary inference: transmembrane proteins

22 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3995339

Approximate Bayesian Computation in Evolution and Ecology

22 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU078

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24557445

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/24557445

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A simulation test bed for hypotheses of genome evolution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24557445

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSU078

1 reference

7 September 2017

1 reference

PMC publication ID

3995339

7 September 2017

PubMed publication ID

24557445

1 reference

PMC publication ID

3995339