A simple, fast, and accurate method of phylogenomic inference (Q21184110)

Dimensions Publication ID

Dimensions

17 August 2022

Martin Wu

1

Martin

Wu

1 reference

Dimensions Publication ID

Dimensions

1023248704

A robust species tree for the alphaproteobacteria

17 August 2022

language of work or name

English

0 references

publication date

2008

0 references

published in

Genome Biology

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volume

9

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issue

10

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page(s)

R151

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cites work

1 reference

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19 March 2017

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Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901

19 March 2017

1 reference

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The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

19 March 2017

1 reference

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

19 March 2017

1 reference

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Horizontal gene transfer among genomes: the complexity hypothesis

19 March 2017

1 reference

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Accelerated evolution and Muller's rachet in endosymbiotic bacteria

19 March 2017

1 reference

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

19 March 2017

1 reference

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Toward Automatic Reconstruction of a Highly Resolved Tree of Life

19 March 2017

1 reference

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

19 March 2017

1 reference

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Environmental genome shotgun sequencing of the Sargasso Sea

19 March 2017

1 reference

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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

19 March 2017

1 reference

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

19 March 2017

1 reference

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Profile hidden Markov models

19 March 2017

1 reference

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Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

19 March 2017

1 reference

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Phylogenomics: the beginning of incongruence?

19 March 2017

1 reference

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Phylogenomics and the reconstruction of the tree of life

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Phylogenetic classification of short environmental DNA fragments

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

A kingdom-level phylogeny of eukaryotes based on combined protein data

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Bacterial rhodopsin: evidence for a new type of phototrophy in the sea

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Phylogenetic diversity and the greedy algorithm.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Missing data, incomplete taxa, and phylogenetic accuracy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

SAR11 clade dominates ocean surface bacterioplankton communities.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Universal trees based on large combined protein sequence data sets.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Phylogenetic inferences from molecular sequences: review and critique

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Alignment-ambiguous nucleotide sites and the exclusion of systematic data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

The genetic data environment an expandable GUI for multiple sequence analysis.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Substitutional bias confounds inference of cyanelle origins from sequence data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Rates of molecular evolution in bacteria are relatively constant despite spore dormancy.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

The closest BLAST hit is often not the nearest neighbor

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Construction of the gyrB Database for the Identification and Classification of Bacteria

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760878

Ribosomal RNA trees misleading?

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18851752

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/GB-2008-9-10-R151

1 reference

Dimensions Publication ID

1023248704

0 references

1 reference

1 reference

PubMed publication ID

18851752

1 reference