(Q34077336)

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Random Addition Concatenation Analysis: a novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the cyanobacteria

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Random Addition Concatenation Analysis: a novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the cyanobacteria (English)

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

1 reference

based on heuristic

inferred from title

1 reference

based on heuristic

inferred from title

Sergios-Orestis Kolokotronis

4

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

5

object named as

Rob DeSalle

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

author name string

Apurva Narechania

1

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Richard H Baker

2

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Ryan Sit

3

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Paul J Planet

6

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

publication date

16 November 2011

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Genome Biology and Evolution

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

4

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

1

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

30-43

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Phylogenomic analysis of marine Roseobacters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Signature proteins for the major clades of Cyanobacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Prokaryotic evolution and the tree of life are two different things

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Gene tree discordance, phylogenetic inference and the multispecies coalescent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Horizontal gene transfer in cyanobacterial signature genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Dealing with incongruence in phylogenomic analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Genome evolution in cyanobacteria: the stable core and the variable shell

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Patterns and implications of gene gain and loss in the evolution of Prochlorococcus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Topological variation in single-gene phylogenetic trees

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

High-resolution species trees without concatenation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Inconsistency of phylogenetic estimates from concatenated data under coalescence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Pattern pluralism and the Tree of Life hypothesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Bushes in the tree of life

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Discordance of species trees with their most likely gene trees.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Highways of gene sharing in prokaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Hidden likelihood support in genomic data: can forty-five wrongs make a right?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Evolutionary origins of genomic repertoires in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Computing prokaryotic gene ubiquity: rescuing the core from extinction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Biased biological functions of horizontally transferred genes in prokaryotic genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

The genome of a motile marine Synechococcus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Partitioned likelihood support and the evaluation of data set conflict

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

The COG database: new developments in phylogenetic classification of proteins from complete genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Lateral gene transfer and the nature of bacterial innovation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Horizontal gene transfer among genomes: the complexity hypothesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Genomic evidence for two functionally distinct gene classes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

The rapid generation of mutation data matrices from protein sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3267395

5 July 2018

Eubacterial phylogeny based on translational apparatus proteins

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVR121

21 January 2018

Robust Locally Weighted Regression and Smoothing Scatterplots

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVR121

21 January 2018

Testing congruence in phylogenomic analysis

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVR121

21 January 2018

How many bootstrap replicates are necessary?

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVR121

21 January 2018

Detection and quantitative assessment of horizontal gene transfer

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVR121

21 January 2018

Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny

1 reference

https://pubmed.ncbi.nlm.nih.gov/22094860

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Confidence Limits on Phylogenies: an Approach using the Bootstrap

1 reference

https://pubmed.ncbi.nlm.nih.gov/22094860

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The origin and evolution of oxygenic photosynthesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/22094860

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/GBE/EVR121

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

ResearchGate publication ID

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