Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences (Q42024436)

15 October 2017

Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences (English)

1 reference

15 October 2017

0 references

0 references

2

Benjamin D Redelings

1 reference

15 October 2017

Sang Chul Choi

1

1 reference

15 October 2017

Jeffrey L Thorne

series ordinal

3

1 reference

15 October 2017

language of work or name

English

0 references

publication date

1 December 2008

1 reference

Philosophical Transactions of the Royal Society B

15 October 2017

1 reference

15 October 2017

363

1 reference

15 October 2017

1512

1 reference

15 October 2017

3931-3939

1 reference

A site- and time-heterogeneous model of amino acid replacement.

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

The distribution of fitness effects of new mutations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Quantifying the impact of protein tertiary structure on molecular 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=2607412

Population genetics without intraspecific data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous 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=2607412

Multilocus association mapping using variable-length Markov chains

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Joint Bayesian Estimation of Alignment 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=2607412

The application of statistical physics to evolutionary biology

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Bayesian coestimation of phylogeny and sequence alignment

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Using equilibrium frequencies in models of 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=2607412

Adaptive evolution of transcription factor binding 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=2607412

Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian 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=2607412

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Protein evolution with dependence among codons due to tertiary structure.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Initial sequencing and analysis of 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=2607412

Building a dictionary for genomes: identification of presumptive regulatory sites by statistical 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=2607412

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic 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=2607412

Pfam: a comprehensive database of protein domain families based on seed alignments

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

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=2607412

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=2607412

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

An evolutionary model for maximum likelihood alignment 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=2607412

Inching toward reality: an improved likelihood model of 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=2607412

Dependence among sites in RNA 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=2607412

Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Simultaneous statistical multiple alignment and phylogeny reconstruction.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Algorithms for variable length Markov chain modeling.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

A "Long Indel" model for evolutionary sequence alignment.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Variations on probabilistic suffix trees: statistical modeling and prediction of protein families.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607412

Site interdependence attributed to tertiary structure in amino acid sequence evolution

17 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18852105

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18852105

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structural constraints and emergence of sequence patterns in protein evolution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18852105

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1098/RSTB.2008.0167

1 reference

15 October 2017

1 reference

15 October 2017

PubMed publication ID

18852105

1 reference