(Q33801888)

29 July 2017

Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins (English)

1 reference

29 July 2017

1 reference

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Blaise Li

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Joao S. Lopes

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Peter G Foster

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Martin Embley

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

4

T Martin Embley

1 reference

29 July 2017

João S Lopes

2

1 reference

PubMed ID

24795089

29 July 2017

Peter G Foster

3

1 reference

29 July 2017

2 May 2014

1 reference

Molecular Biology and Evolution

29 July 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

volume

31

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

page(s)

1697-1709

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions

2 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Diversity and evolutionary history of plastids and their hosts

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

HMMER web server: interactive sequence similarity searching

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Resolving difficult phylogenetic questions: why more sequences are not enough

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Differential gene retention in plastids of common recent origin.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Biopython: freely available Python tools for computational molecular biology and bioinformatics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

The archaebacterial origin of eukaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

An empirical codon model for protein sequence evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Phylogenomics: the beginning of incongruence?

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

ProtTest: selection of best-fit models of protein evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Modeling compositional heterogeneity

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Evolution: red algal genome affirms a common origin of all plastids

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

MUSCLE: multiple sequence alignment with high accuracy and high throughput

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Protein import into cyanelles

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Mutation pressure, natural selection, and the evolution of base composition in Drosophila

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

The general stochastic model of nucleotide substitution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069611

Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria.

4 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Metabolic symbiosis and the birth of the plant kingdom

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Dating the cyanobacterial ancestor of the chloroplast

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

PHYLOGENY ESTIMATION AND HYPOTHESIS TESTING USING MAXIMUM LIKELIHOOD

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

The origin of red algae and the evolution of chloroplasts

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Is convergence surprising? An examination of the frequency of convergence in simulated datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Single, ancient origin of a plastid metabolite translocator family in Plantae from an endomembrane-derived ancestor

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Evidence for a common origin of chloroplasts with light-harvesting complexes of different pigmentation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU105

Phylogenetic estimation under codon models can be biased by codon usage heterogeneity

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24795089

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSU105

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24795089%20AND%20SRC:MED&resulttype=core&format=json