(Q36830858)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

title

CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

1 reference

Marcelo Serrano Zanetti

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

author name string

Manuel Gil

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

Stefan Zoller

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

Maria Anisimova

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

publication date

23 February 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

Molecular Biology and Evolution

24 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

volume

30

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

page(s)

1270-1280

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

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

24 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

The Pfam protein families database

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Complex interplay of evolutionary forces in the ladybird homeobox genes of Drosophila melanogaster

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

OMA 2011: orthology inference among 1000 complete genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Correcting the bias of empirical frequency parameter estimators in codon models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Estimates of the effect of natural selection on protein-coding content

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Pathological rate matrices: from primates to pathogens

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Pitfalls of the most commonly used models of context dependent substitution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Investigating protein-coding sequence evolution with probabilistic codon substitution models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Bayesian comparisons of codon substitution models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: from plants to bacteria?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

BEAST: Bayesian evolutionary analysis by sampling trees

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

PAML 4: phylogenetic analysis by maximum likelihood

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

An empirical codon model for protein sequence evolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Empirical codon substitution matrix

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

A space-time process model for the evolution of DNA sequences.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

A combined empirical and mechanistic codon model.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

A new look at the statistical model identification

5 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST034

The Scaling and Squaring Method for the Matrix Exponential Revisited

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST034

Nineteen Dubious Ways to Compute the Exponential of a Matrix, Twenty-Five Years Later

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST034

Estimating the Dimension of a Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMST034

A novel use of equilibrium frequencies in models of sequence evolution

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649670

Empirical analysis of the most relevant parameters of codon substitution models

20 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23436912

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23436912

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Betweenness preference: quantifying correlations in the topological dynamics of temporal networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23436912

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MST034

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json

24 February 2020

PubMed publication ID

23436912

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23436912%20AND%20SRC:MED&resulttype=core&format=json