OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics (Q21093422)

5 August 2022

5

Marie-Ka Tilak

Marie-Ka

Tilak

1 reference

5 August 2022

1

Vincent

Ranwez

Vincent Ranwez

1 reference

5 August 2022

Sylvie Ranwez

3

Sylvie

Ranwez

1 reference

1026589476

5 August 2022

Khalid Belkhir

series ordinal

4

author given names

Khalid

author last names

Belkhir

1 reference

1026589476

5 August 2022

Emmanuel Jp Douzery

series ordinal

6

author given names

Emmanuel JP

author last names

Douzery

1 reference

1026589476

Multiple molecular evidences for a living mammalian fossil

5 August 2022

language of work or name

English

0 references

publication date

2007

0 references

published in

BMC Evolutionary Biology

0 references

volume

7

0 references

issue

1

0 references

page(s)

241

0 references

cites work

1 reference

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Using genomic data to unravel the root of the placental mammal phylogeny

19 March 2017

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Early history of mammals is elucidated with the ENCODE multiple species sequencing data

19 March 2017

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19 March 2017

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Retroposed elements as archives for the evolutionary history of placental mammals

19 March 2017

1 reference

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OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

19 March 2017

1 reference

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transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences

19 March 2017

1 reference

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Inparanoid: a comprehensive database of eukaryotic orthologs

19 March 2017

1 reference

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

19 March 2017

1 reference

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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

19 March 2017

1 reference

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MODELTEST: testing the model of DNA substitution

19 March 2017

1 reference

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Evolutionary trees from DNA sequences: A maximum likelihood approach

19 March 2017

1 reference

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Phylogenomics and the reconstruction of the tree of life

19 March 2017

1 reference

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A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships

19 March 2017

1 reference

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Resolution of the early placental mammal radiation using Bayesian phylogenetics

19 March 2017

1 reference

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Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes

19 March 2017

1 reference

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Molecular phylogenetics and the origins of placental mammals

19 March 2017

1 reference

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Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules

19 March 2017

1 reference

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The guinea-pig is not a rodent

19 March 2017

1 reference

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A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly

19 March 2017

1 reference

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Rooting the eutherian tree: the power and pitfalls of phylogenomics

19 March 2017

1 reference

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Genomics, biogeography, and the diversification of placental mammals

19 March 2017

1 reference

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A phylogenomic study of human, dog, and mouse

19 March 2017

1 reference

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The ENCODE (ENCyclopedia Of DNA Elements) Project

19 March 2017

1 reference

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Among-site rate variation and its impact on phylogenetic analyses

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Mammalian phylogenomics comes of age

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

The Ensembl automatic gene annotation system

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Parallel adaptive radiations in two major clades of placental mammals

7 April 2017

1 reference

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Evolution of the cytochrome b gene of mammals

7 April 2017

1 reference

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Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

The effect of branch lengths on phylogeny: an empirical study using highly conserved orthologs from mammalian genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

The ENCODE Project at UC Santa Cruz

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Endemic African mammals shake the phylogenetic tree

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Evidence on mammalian phylogeny from sequences of exon 28 of the von Willebrand factor gene

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Dog as an outgroup to human and mouse

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Assessing performance of orthology detection strategies applied to eukaryotic genomes

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

The root of the mammalian tree inferred from whole mitochondrial genomes

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Profiling phylogenetic informativeness

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

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

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Rabbits, if anything, are likely Glires

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Sequence gaps join mice and men: phylogenetic evidence from deletions in two 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=2249597

On the best evolutionary rate for phylogenetic analysis.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Phylogenetic information and experimental design in molecular systematics.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2249597

Estimating the pattern of nucleotide substitution

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18053139

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Rates of genome evolution and branching order from whole genome analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18053139

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2148-7-241

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-7-241

1 reference

9 September 2019

1 reference

1 reference

PubMed publication ID

18053139

1 reference