(Q33393406)

26 July 2017

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny (English)

1 reference

26 July 2017

1 reference

4

Andrew J Roger

1 reference

26 July 2017

1

Huai-Chun Wang

1 reference

26 July 2017

Karen Li

2

1 reference

PubMed ID

19087270

26 July 2017

Edward Susko

series ordinal

3

1 reference

26 July 2017

16 December 2008

1 reference

26 July 2017

BMC Evolutionary Biology

1 reference

26 July 2017

8

1 reference

26 July 2017

331

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-8-331

26 July 2017

0 references

cites work

An improved general amino acid replacement matrix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Different versions of the Dayhoff rate matrix

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Protein evolution with dependence among codons due to tertiary structure.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Microsporidia: Biology and Evolution of Highly Reduced Intracellular Parasites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

An expectation maximization algorithm for training hidden substitution models.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Hidden Markov models for detecting remote protein homologies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Profile analysis: detection of distantly related proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

The rapid generation of mutation data matrices from protein sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Amino acid substitution matrices from protein blocks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Empirical profile mixture models for phylogenetic reconstruction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Frequent and widespread parallel evolution of protein sequences

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Topological estimation biases with covarion evolution.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

On reduced amino acid alphabets for phylogenetic inference.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Testing for covarion-like evolution in protein sequences.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

A transition probability model for amino acid substitutions from blocks.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Using protein structural information in evolutionary inference: transmembrane proteins

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2628903

Model of amino acid substitution in proteins encoded by mitochondrial DNA

31 October 2018

1 reference

12 December 2020

Modeling residue usage in aligned protein sequences via maximum likelihood

1 reference

12 December 2020

Models of natural mutations including site heterogeneity

1 reference

12 December 2020

Site interdependence attributed to tertiary structure in amino acid sequence evolution

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2148-8-331

1 reference

PubMed ID

19087270

Dimensions Publication ID

26 July 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-8-331

9 September 2019

1 reference

26 July 2017

1 reference

PubMed ID

19087270