(Q41966236)

14 October 2017

Phylogenetic mixture models for proteins (English)

1 reference

14 October 2017

1 reference

Si Quang Le

1

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14 October 2017

Nicolas Lartillot

series ordinal

2

1 reference

14 October 2017

Olivier Gascuel

series ordinal

3

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14 October 2017

language of work or name

English

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publication date

1 December 2008

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14 October 2017

12

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Philosophical Transactions of the Royal Society B

inferred from page(s)

published in

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14 October 2017

363

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14 October 2017

3965-3976

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14 October 2017

1512

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An improved general amino acid replacement matrix

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

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=2607422

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

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=2607422

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies 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=2607422

An expectation maximization algorithm for training hidden 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=2607422

The Pfam protein families 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=2607422

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

Selection of conserved blocks from multiple alignments for their use in 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=2607422

PASSML: combining evolutionary inference and protein secondary structure prediction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

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=2607422

Modeling the covarion hypothesis of nucleotide substitution.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence 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=2607422

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=2607422

Context-dependent optimal substitution matrices

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

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=2607422

A mutation data matrix for transmembrane proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

Evolutionary trees from DNA sequences: A maximum likelihood approach

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

The neighbor-joining method: a new method for reconstructing phylogenetic trees

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

The rapid generation of mutation data matrices from protein 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=2607422

Empirical profile mixture models for phylogenetic 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=2607422

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

An alternative model of amino acid replacement

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

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=2607422

Combining protein evolution and secondary structure

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2607422

Modeling residue usage in aligned protein sequences via maximum likelihood

18 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18852096

12 December 2020

inferred from PubMed ID database lookup

The HSSP database of protein structure-sequence alignments

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18852096

12 December 2020

inferred from PubMed ID database lookup

Models of natural mutations including site heterogeneity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18852096

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1098/RSTB.2008.0180

1 reference

14 October 2017

1 reference

14 October 2017

1 reference