(Q42042437)

15 October 2017

Estimating empirical codon hidden Markov models (English)

1 reference

15 October 2017

2

1 reference

15 October 2017

Nicola De Maio

1

0 references

Christian Schlötterer

series ordinal

3

object named as

Christian Schlötterer

1 reference

15 October 2017

Carolin Kosiol

4

1 reference

15 October 2017

27 November 2012

1 reference

Molecular Biology and Evolution

15 October 2017

1 reference

15 October 2017

30

1 reference

15 October 2017

3

1 reference

15 October 2017

725-736

1 reference

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Pervasive multinucleotide mutational events in eukaryotes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

CodonTest: modeling amino acid substitution preferences in coding sequences

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Positive selection differs between protein secondary structure elements in Drosophila

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Investigating protein-coding sequence evolution with probabilistic codon substitution models

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

The quest for natural selection in the age of comparative genomics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

PAML 4: phylogenetic analysis by maximum likelihood

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

An empirical codon model for protein sequence evolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

XRate: a fast prototyping, training and annotation tool for phylo-grammars

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Bayes empirical bayes inference of amino acid sites under positive selection

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Estimating the frequency of events that cause multiple-nucleotide changes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Combining phylogenetic and hidden Markov models in biosequence analysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Statistical methods for detecting molecular adaptation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

A Hidden Markov Model approach to variation among sites in rate of evolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

Dynamic evolution of the innate immune system in Drosophila.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

A combined empirical and mechanistic codon model.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3563974

A new look at the statistical model identification

17 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS266

Estimating the Dimension of a Model

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS266

Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSS266

A Low Rate of Simultaneous Double-Nucleotide Mutations in Primates

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23188590

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSS266

1 reference

15 October 2017

1 reference

PMC publication ID

3563974

15 October 2017

PubMed publication ID

23188590

1 reference

PMC publication ID

3563974