Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: case studies with diploblast LSU. (Q33282873)

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

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scholarly article

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Europe PubMed Central

PubMed publication ID

25 July 2017

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

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25 July 2017

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Oliver Voigt

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Gert Wörheide

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Europe PubMed Central

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25 July 2017

6

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John N A Hooper

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25 July 2017

Scott A Nichols

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Scott A Nichols

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Dirk Erpenbeck

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Bernard M Degnan

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Martin Dohrmann

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25 July 2017

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24 April 2007

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25 July 2017

Journal of Molecular Evolution

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25 July 2017

64

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Europe PubMed Central

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25 July 2017

5

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Europe PubMed Central

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25 July 2017

543-557

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Europe PubMed Central

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25 July 2017

Phylogenetic analysis of the Hsp70 sequences reveals the monophyly of Metazoa and specific phylogenetic relationships between animals and fungi

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21 January 2018

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

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A new perspective on lower metazoan relationships from 18S rDNA sequences

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Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals

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21 January 2018

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

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12 December 2020

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Computing Bayes factors using thermodynamic integration

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https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Evolutionary analyses of DNA sequences subject to constraints of secondary structure

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https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA.

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https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Phylogeny and classification of lithistid sponges (porifera: Demospongiae): a preliminary assessment using ribosomal DNA sequence comparisons.

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https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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A Stochastic Model for the Evolution of Autocorrelated DNA Sequences

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https://pubmed.ncbi.nlm.nih.gov/17460808

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Highlights of marine natural products chemistry (1972-1999).

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https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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The European large subunit ribosomal RNA database

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https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites

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https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Evolutionary relationships of Metazoa within the eukaryotes based on molecular data from Porifera

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Purine-purine mismatches in RNA helices: evidence for protonated G.A pairs and next-nearest neighbor effects

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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MrBayes 3: Bayesian phylogenetic inference under mixed models

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https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Bayesian phylogenetic analysis of combined data

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Phylogeny and evolution of calcareous sponges: monophyly of calcinea and calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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G.U base pairing motifs in ribosomal RNA.

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Estimating substitution rates in ribosomal RNA genes.

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Is it better to add taxa or characters to a difficult phylogenetic problem?

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Bayesian inference of phylogeny and its impact on evolutionary biology

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Comparative analysis of Brachyury T-domains, with the characterization of two new sponge sequences, from a hexactinellid and a calcisponge

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Phylogenetic position of the Hexactinellida within the phylum Porifera based on the amino acid sequence of the protein kinase C from Rhabdocalyptus dawsoni

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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RNA secondary structure: physical and computational aspects

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I.

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

based on heuristic

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Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution

1 reference

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12 December 2020

based on heuristic

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An analysis of partial 28S ribosomal RNA sequences suggests early radiations of sponges

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Order level differences in the structure of partial LSU across demosponges (Porifera): new insights into an old taxon.

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Evaluating multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Phylogenetic analysis of Rhinosporidium seeberi's 18S small-subunit ribosomal DNA groups this pathogen among members of the protoctistan Mesomycetozoa clade

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae).

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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The importance of proper model assumption in bayesian phylogenetics

1 reference

https://pubmed.ncbi.nlm.nih.gov/17460808

12 December 2020

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Multiple sequence alignment with Clustal X

1 reference

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12 December 2020

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Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA.

1 reference

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12 December 2020

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Dependence among sites in RNA evolution

1 reference

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12 December 2020

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Identifiability of parameters in MCMC Bayesian inference of phylogeny

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RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences

1 reference

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12 December 2020

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Reassessment of homology of morphological characters in tetractinellid sponges based on molecular data

1 reference

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1 reference

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12 December 2020

based on heuristic

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10.1007/S00239-006-0146-3

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Europe PubMed Central

PubMed publication ID

25 July 2017

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PubMed publication ID

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Europe PubMed Central

PubMed publication ID

25 July 2017

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