An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models (Q21283842)

18 August 2022

1

Georgia Tsagkogeorga

Georgia

Tsagkogeorga

1 reference

18 August 2022

8

Dorothée Huchon

Dorothée

Huchon

1 reference

18 August 2022

Xavier Turon

2

Xavier

Turon

1 reference

18 August 2022

Yossi Loya

7

Yossi

Loya

1 reference

18 August 2022

4

Marie-Ka Tilak

Marie-Ka

Tilak

1 reference

18 August 2022

Emmanuel J.P. Douzery

9

Emmanuel J P Douzery

Emmanuel JP

Douzery

1 reference

18 August 2022

6

Noa

Shenkar

Noa Shenkar

1 reference

18 August 2022

Russell R Hopcroft

3

Russell R

Hopcroft

1 reference

18 August 2022

Tamar Feldstein

series ordinal

5

author given names

Tamar

author last names

Feldstein

1 reference

18 August 2022

language of work or name

English

0 references

publication date

2009

0 references

published in

BMC Evolutionary Biology

0 references

volume

9

0 references

issue

1

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page(s)

187

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cites work

The Vienna RNA websuite

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

MAFFT version 5: improvement in accuracy of multiple sequence alignment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

RETRACTED: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

The European ribosomal RNA database

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Seeing chordate evolution through the Ciona genome sequence

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Additional molecular support for the new chordate phylogeny

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

The amphioxus genome and the evolution of the chordate karyotype

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Broad phylogenomic sampling improves resolution of the animal 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=2739199

Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Tunicates and not cephalochordates are the closest living relatives of vertebrates

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

MrBayes 3: Bayesian phylogenetic inference under mixed models

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Selection of conserved blocks from multiple alignments for their use in phylogenetic 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=2739199

MODELTEST: testing the model of DNA substitution

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Embryology of a planktonic tunicate reveals traces of sessility

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Molecular evolution of rDNA in early diverging Metazoa: first comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

12 September 2017

The road to modularity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: case studies with diploblast LSU.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state 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=2739199

Ascidian molecular phylogeny inferred from mtDNA data with emphasis on the Aplousobranchiata

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Phylogenetic position of a deep-sea ascidian, Megalodicopia hians, inferred from the molecular 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=2739199

The Ciona intestinalis genome: when the constraints are off.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Urochordates are monophyletic within the deuterostomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA 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=2739199

RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

The simple tail of chordates: phylogenetic significance of appendicularians

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Tunicate tails, stolons, and the origin of the vertebrate trunk

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in 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=2739199

Multiple origins of the ascidian-Prochloron symbiosis: molecular phylogeny of photosymbiotic and non-symbiotic colonial ascidians inferred from 18S rDNA sequences

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Coloniality has evolved once in Stolidobranch Ascidians.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Phylogeny of the families Pyuridae and Styelidae (Stolidobranchiata, Ascidiacea) inferred from mitochondrial and nuclear DNA sequences.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Phylogeny and evolution of glass sponges (porifera, hexactinellida).

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Computing Bayes factors using thermodynamic integration.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Sampling properties of the bootstrap support in molecular phylogeny: influence of nonindependence among sites

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

RnaViz 2: an improved representation of RNA secondary structure.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Phylogeny of Tunicata inferred from molecular and morphological characters

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

Evolutionary history of free-swimming and sessile lifestyles in urochordates as deduced from 18S rDNA molecular phylogeny

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739199

The evolution of anural larvae in molgulid ascidians

29 November 2018

1 reference

12 December 2020

Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis

1 reference

12 December 2020

Genetics of actin-related sequences in tomato

1 reference

12 December 2020

Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2148-9-187

1 reference

0 references

1 reference

1 reference

PubMed publication ID

19656395

1 reference