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Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

http://www.wikidata.org/entity/Q33650399

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A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data Considerations For Optimizing Microbiome Analysis Using a Marker Gene Use of ITS2 region as the universal DNA barcode for plants and animals Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies The changing epitome of species identification - DNA barcoding Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: evidence from case studies in the Metazoa Identification of commercial Ganoderma (Lingzhi) species by ITS2 sequences Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae).A non-toxigenic but morphologically and phylogenetically distinct new species of Pseudo-nitzschia, P. sabit sp. nov. (Bacillariophyceae).Chodatodesmus australis sp. nov. (Scenedesmaceae, Chlorophyta) from Antarctica, with the emended description of the genus Chodatodesmus, and circumscription of Flechtneria rotunda gen. et sp. nov.Three novel species in the Pseudo-nitzschia pseudodelicatissima complex: P. batesiana sp. nov., P. lundholmiae sp. nov., and P. fukuyoi sp. nov. (Bacillariophyceae) from the Strait of Malacca, Malaysia.Tetraflagellochloris mauritanica gen. et sp. nov. (Chlorophyceae), a New Flagellated Alga from the Mauritanian Desert: Morphology, Ultrastructure, and Phylogenetic Framing.High diversity of Pseudo-nitzschia along the northern coast of Sarawak (Malaysian Borneo), with descriptions of P. bipertita sp. nov. and P. limii sp. nov. (Bacillariophyceae).Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life Barcode ITS2: a useful tool for identifying Trachelospermum jasminoides and a good monitor for medicine market.A close-up view on ITS2 evolution and speciation - a case study in the Ulvophyceae (Chlorophyta, Viridiplantae).Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants.Composition of epiphytic bacterial communities differs on petals and leaves.Molecular taxonomy of Dunaliella (Chlorophyceae), with a special focus on D. salina: ITS2 sequences revisited with an extensive geographical sampling.Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota).Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree.Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2 ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding.Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum Secondary structure improves OTU assignments of 16S rRNA gene sequences.The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS.Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.Secondary structure of nrDNA Internal Transcribed Spacers as a useful tool to align highly divergent species in phylogenetic studies.bcgTree: automatized phylogenetic tree building from bacterial core genomes.ITS2 Database V: Twice as Much.Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure.ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae).PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities.The ITS2 Database.DCJ-RNA - double cut and join for RNA secondary structures.New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida).Molecular characterization of pouched amphistome parasites (Trematoda: Gastrothylacidae) using ribosomal ITS2 sequence and secondary structures.

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Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

http://www.wikidata.org/entity/Q33650399

description

2010 nî lūn-bûn

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2010 թուականի Յունուարին հրատարակուած գիտական յօդուած

@hyw

2010 թվականի հունվարին հրատարակված գիտական հոդված

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2010年の論文

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2010年論文

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2010年論文

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2010年論文

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2010年論文

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2010年論文

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2010年论文

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name

Including RNA secondary struct ...... truction of phylogenetic trees

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Including RNA secondary struct ...... truction of phylogenetic trees

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type

label

Including RNA secondary struct ...... truction of phylogenetic trees

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Including RNA secondary struct ...... truction of phylogenetic trees

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prefLabel

Including RNA secondary struct ...... truction of phylogenetic trees

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Including RNA secondary struct ...... truction of phylogenetic trees

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Including RNA secondary struct ...... truction of phylogenetic trees

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Jörg Schultz

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Matthias Wolf

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Tobias Müller

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P2860

Nuclear and mitochondrial data reveal different evolutionary processes in the Lake Tanganyika cichlid genus Tropheus

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya

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

4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing

Molecular phylogenetics: state-of-the-art methods for looking into the past.

Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals

ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales).

Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE.

ITS2 is a double-edged tool for eukaryote evolutionary comparisons.

Pan-eukaryote ITS2 homologies revealed by RNA secondary structure.

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scholarly article

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10.1186/1745-6150-5-4

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Thomas Dandekar

Alexander Keller

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41038534

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1049429807

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20078867

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2821295

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