Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach (Q35914100)

11 August 2017

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach (English)

1 reference

11 August 2017

1 reference

1 reference

11 August 2017

Adi Doron-Faigenboim

0 references

Eran Bacharach

0 references

Eric Martz

0 references

Adi Stern

1 reference

11 August 2017

Adi Doron-Faigenboim

series ordinal

1 reference

11 August 2017

Elana Erez

series ordinal

1 reference

11 August 2017

language of work or name

English

0 references

publication date

22 June 2007

1 reference

11 August 2017

Nucleic Acids Research

1 reference

11 August 2017

1 reference

11 August 2017

Web Server issue

1 reference

11 August 2017

W506-11

1 reference

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Natural selection on protein-coding genes in the human genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Initial sequence of the chimpanzee genome and comparison with the human genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

The power of phylogenetic comparison in revealing protein function

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Not so different after all: a comparison of methods for detecting amino acid sites under selection

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Bayes empirical bayes inference of amino acid sites under positive selection

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

A single amino acid change in the SPRY domain of human Trim5alpha leads to HIV-1 restriction

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Selecton: a server for detecting evolutionary forces at a single amino-acid site

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Retrovirus resistance factors Ref1 and Lv1 are species-specific variants of TRIM5alpha

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

BTBD1 and BTBD2 colocalize to cytoplasmic bodies with the RBCC/tripartite motif protein, TRIM5delta

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Restriction of multiple divergent retroviruses by Lv1 and Ref1

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

The tripartite motif family identifies cell compartments

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

PAML: a program package for phylogenetic analysis by maximum likelihood

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

The rapid generation of mutation data matrices from protein sequences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

A combined empirical and mechanistic codon model.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

The influence of phylogenetic uncertainty on the detection of positive Darwinian selection.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

A gamma mixture model better accounts for among site rate heterogeneity

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

BADASP: predicting functional specificity in protein families using ancestral sequences.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Bayesian estimation of positively selected sites

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

A structural EM algorithm for phylogenetic inference.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Site-Specific Evolutionary Rate Inference: Taking Phylogenetic Uncertainty into Account

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933148

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution

14 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17586822

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Pervasive adaptive evolution in mammalian fertilization proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17586822

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17586822

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKM382

1 reference

journals/nar/SternDEMBP07

11 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

11 August 2017

PubMed publication ID

17586822

1 reference