(Q28765455)

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An application of supertree methods to Mammalian mitogenomic sequences

scientific article (publication date: 12 May 2010)

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An application of supertree methods to Mammalian mitogenomic sequences (English)

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author name string

Véronique Campbell

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François-Joseph Lapointe

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publication date

12 May 2010

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Evolutionary Bioinformatics

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6

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57-71

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Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments

1 reference

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16 March 2017

Broad phylogenomic sampling improves resolution of the animal tree of life

1 reference

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16 March 2017

Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset

1 reference

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16 March 2017

Rooting the eutherian tree: the power and pitfalls of phylogenomics

1 reference

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16 March 2017

Genomics, biogeography, and the diversification of placental mammals

1 reference

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16 March 2017

The adequacy of morphology for reconstructing the early history of placental mammals

1 reference

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16 March 2017

The delayed rise of present-day mammals

1 reference

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16 March 2017

Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus

1 reference

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16 March 2017

Site specific rates of mitochondrial genomes and the phylogeny of eutheria

1 reference

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16 March 2017

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

1 reference

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16 March 2017

Missing data and the design of phylogenetic analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

16 March 2017

Phylogenomics and the reconstruction of 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=2880846

16 March 2017

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

1 reference

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16 March 2017

Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling

1 reference

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16 March 2017

MRBAYES: Bayesian inference of phylogenetic trees

1 reference

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16 March 2017

MODELTEST: testing the model of DNA substitution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

16 March 2017

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

16 March 2017

Evolutionary trees from DNA sequences: A maximum likelihood approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

16 March 2017

CLUSTAL: a package for performing multiple sequence alignment on a microcomputer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

16 March 2017

APE: Analyses of Phylogenetics and Evolution in R language

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

7 April 2017

Genome-scale approaches to resolving incongruence in molecular phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

7 April 2017

A new method for calculating evolutionary substitution rates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

7 April 2017

Molecules consolidate the placental mammal tree

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

7 April 2017

Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

7 April 2017

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

7 April 2017

The general stochastic model of nucleotide substitution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

7 April 2017

Combining data in phylogenetic analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Mitogenomic relationships of placental mammals and molecular estimates of their divergences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Resolving animal phylogeny: a sledgehammer for a tough nut?

1 reference

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3 June 2018

Mammalian evolution and biomedicine: new views from phylogeny

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Properties of supertree methods in the consensus setting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

The supermatrix approach to systematics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

The evolution of supertrees.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

The shape of supertrees to come: tree shape related properties of fourteen supertree methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Supertree construction in the genomic age.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Prospects for building the tree of life from large sequence databases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Evolution. Genomic databases and 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=2880846

3 June 2018

Clann: investigating phylogenetic information through supertree analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations

1 reference

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3 June 2018

The root of the mammalian tree inferred from whole mitochondrial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Assessment of the accuracy of matrix representation with parsimony analysis supertree construction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Does adding characters with missing data increase or decrease phylogenetic accuracy?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Combining data sets with different phylogenetic histories

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Maximum-likelihood estimation of evolutionary trees from continuous characters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

3 June 2018

Reply from J.P. Huelsenbeck, J.J. Bull and C.W. Cunningham

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Total evidence, average consensus and matrix representation with parsimony: what a difference distances make.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

SDM: a fast distance-based approach for (super) tree building in phylogenomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods

1 reference

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27 November 2018

Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia

1 reference

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27 November 2018

Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

War and peace in phylogenetics: a rejoinder on total evidence and consensus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Phylogenetics. Which mammalian supertree to bark up?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Rodent monophyly: pitfalls of molecular phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

The agreement metric for labeled binary trees.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880846

27 November 2018

Total evidence, consensus, and bat phylogeny: A distance-based approach

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Resolution of a supertree/supermatrix paradox

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Matrix representation in reconstructing phylogenetic relationships among the eukaryotes

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Phylogenetic inference based on matrix representation of trees

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Trees versus characters and the supertree/supermatrix "paradox"

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Rates of genome evolution and branching order from whole genome analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Phylogenetic supertrees: Assembling the trees of life

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ANALYZING TABLES OF STATISTICAL TESTS

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The platypus put in its place

1 reference

https://pubmed.ncbi.nlm.nih.gov/20535231

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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