(Q41882061)

13 October 2017

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

1 reference

13 October 2017

0 references

2

1 reference

13 October 2017

Carolin Kosiol

1

1 reference

PMC publication ID

3157587

13 October 2017

language of work or name

English

0 references

publication date

21 June 2011

1 reference

Journal of Molecular Biology

13 October 2017

1 reference

13 October 2017

411

1 reference

13 October 2017

4

1 reference

13 October 2017

910-923

1 reference

INDELible: a flexible simulator of biological sequence evolution

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

An improved general amino acid replacement matrix

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

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=3157587

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=3157587

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=3157587

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=3157587

Simultaneous inference of selection and population growth from patterns of variation in the human genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Different versions of the Dayhoff rate matrix

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

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=3157587

SIFT: Predicting amino acid changes that affect protein function

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

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=3157587

Selection in the evolution of gene duplications

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

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=3157587

Towards a structural basis of human non-synonymous single nucleotide polymorphisms

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Models of molecular evolution and phylogeny

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Assessing the impact of secondary structure and solvent accessibility on protein 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=3157587

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=3157587

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Exhaustive matching of the entire protein sequence database

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Amino acid substitution matrices from protein blocks

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Detecting amino acid sites under positive selection and purifying 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=3157587

Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Using protein structural information in evolutionary inference: transmembrane proteins

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Amino acid substitution during functionally constrained divergent evolution of protein sequences.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

A novel use of equilibrium frequencies in models of sequence evolution

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

[Evaluation and extension of Markov process models for the evolution of DNA]

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3157587

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites

3 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21718704

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Model of amino acid substitution in proteins encoded by mitochondrial DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21718704

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21718704

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.JMB.2011.06.005

1 reference

13 October 2017

1 reference

PMC publication ID

3157587

13 October 2017

PubMed publication ID

21718704

1 reference

PMC publication ID

3157587