Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules.

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Molecular Phylogenetics and Evolution

• Publication date

  2004-12-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/J.YMPEV.2004.08.004PMID 15522814
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae).

  2004cited by this paper
• A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae)

  2004cited by this paper
• NEW DEVELOPMENTS IN THE BIOLOGY OF CHRYSOMELIDAE

  2004cited by this paper
• The evolution of cucurbitacin pharmacophagy in rootworms: insight from Luperini paraphyly

  2004cited by this paper
• RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences.

  2003cited by this paper
• Comparison between molecular and morphological-based phylogenies of galerucine/alticine leaf beetles (Coleoptera: Chrysomelidae)

  2003cited by this paper
• Convergent evolution of cucurbitacin feeding in spatially isolated rootworm taxa (Coleoptera: Chrysomelidae; Galerucinae, Luperini).

  2003cited by this paper
• 18S ribosomal RNA and tetrapod phylogeny.

  2003cited by this paper
• ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae.

  2003cited by this paper
• Phylogeny and evolution of calcareous sponges: monophyly of calcinea and calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry.

  2003cited by this paper
• Louse (Insecta: Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable

  2002cited by this paper
• Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution.

  2002cited by this paper
• The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

  2002cited by this paper
• Unalignable sequences and molecular evolution

  2001cited by this paper
• RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.

  2001cited by this paper
• Phylogeny of Trichoptera (caddisflies): characterization of signal and noise within multiple datasets.

  2001cited by this paper
• How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction.

  2000cited by this paper
• Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae).

  2000cited by this paper
• Secondary Structural and Phylogenetic Implications of Nuclear Large Subunit Ribosomal RNA in the Ectomycorrhizal Fungus Tricholoma matsutake

  2000cited by this paper
• SEQUENCE AND SECONDARY STRUCTURE VARIATION IN THE GYRODACTYLUS (PLATYHELMINTHES: MONOGENEA) RIBOSOMAL RNA GENE ARRAY

  2000cited by this paper
• The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence.

  2000cited by this paper
• Use of RNA Secondary Structure for Studying the Evolution of RNase P and RNase MRP

  2000cited by this paper
• Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains.

  2000cited by this paper
• Cirripede phylogeny using a novel approach: molecular morphometrics.

  2000cited by this paper
• Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses.

  2000cited by this paper
• RNA secondary structure: physical and computational aspects

  2000cited by this paper
• Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.

  2000cited by this paper
• Long Branch Attraction Effects and the Status of “Basal Eukaryotes”: Phylogeny and Structural Analysis of the Ribosomal RNA Gene Cluster of the Free-living Diplomonad Trepomonas agilis

  2000cited by this paper
• Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures.

  2000cited by this paper
• 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, hemiptera).

  2000cited by this paper
• Phylogenetic relationships of the genus Frenkelia: a review of its history and new knowledge gained from comparison of large subunit ribosomal ribonucleic acid gene sequences.

  1999cited by this paper
• A Probabilistic Treatment of Phylogeny and Sequence Alignment

  1999cited by this paper
• Estimating the Contributions of Selection and Self-Organization in RNA Secondary Structure

  1999cited by this paper
• Fixed Character States and the Optimization of Molecular Sequence Data

  1999cited by this paper
• The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans.

  1998cited by this paper
• Comparison of the nucleotide sequence and secondary structure of the 5.8S ribosomal RNA gene of Chlamydomonas tetragama with those of green algae.

  1998cited by this paper
• Molecular phylogenetics at the Felsenstein zone: approaching the Strepsiptera problem using 5.8S and 28S rDNA sequences.

  1998cited by this paper
• RAGA: RNA sequence alignment by genetic algorithm.

  1997cited by this paper
• Conserved Primary and Secondary Structural Motifs of Amphibian 12S rRNA, Domain III

  1997cited by this paper
• Systematics of Nothofagus (Nothofagaceae) based on rDNA spacer sequences (ITS): taxonomic congruence with morphology and plastid sequences.

  1997cited by this paper
• Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa.

  1997cited by this paper
• Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules

  1996cited by this paper
• Internal transcribed spacer sequences from 38 recognized species of Suillus sensu lato: Phylogenetic and taxonomic implications

  1996cited by this paper
• Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA.

  1996cited by this paper
• Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA.

  1996cited by this paper
• Molecular homology assessment and phylogeny in the lizard family opluridae (Squamata: Iguania).

  1996cited by this paper
• CRAYFISH MOLECULAR SYSTEMATICS: USING A COMBINATION OF PROCEDURES TO ESTIMATE PHYLOGENY

  1996cited by this paper
• Evolution according to large ribosomal subunit RNA.

  1995cited by this paper
• Evolution according to large ribosomal subunit RNA

  1995cited by this paper
• Molecular evolution of the mitochondrial 12S rRNA in Ungulata (mammalia)

  1995cited by this paper
• Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs.

  1995cited by this paper
• PHYLOGENETIC DIVERSITY IN SHIITAKE INFERRED FROM NUCLEAR RIBOSOMAL DNA SEQUENCES

  1995cited by this paper
• Erratum: The ITS Region of Nuclear Ribosomal DNAZ: A Valuable Source of Evidence on Angiosperm Phylogeny

  1995cited by this paper
• Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals.

  1995cited by this paper
• Fast folding and comparison of RNA secondary structures

  1994cited by this paper
• Molecular systematics of hystricognath rodents: evidence from the mitochondrial 12S rRNA gene.

  1994cited by this paper
• RATE LIMITS FOR MISPAIRING AND COMPENSATORY CHANGE: THE MITOCHONDRIAL RIBOSOMAL DNA OF ANTELOPES

  1994cited by this paper
• Mosquito large subunit ribosomal RNA: simultaneous alignment of primary and secondary structure.

  1994cited by this paper
• Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.

  1994cited by this paper
• Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis.

  1993cited by this paper
• Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: Calibration of the molecular clock

  1993cited by this paper
• Rates and patterns of base change in the small subunit ribosomal RNA gene.

  1993cited by this paper
• Mispairing and compensational changes during the evolution of mitochondrial ribosomal RNA.

  1992cited by this paper
• Substitution bias, weighted parsimony, and amniote phylogeny as inferred from 18S rRNA sequences.

  1992cited by this paper
• Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA.

  1991cited by this paper
• Ribosomal DNA: Molecular Evolution and Phylogenetic Inference

  1991cited by this paper
• Comparing multiple RNA secondary structures using tree comparisons

  1990cited by this paper
• Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications.

  1988cited by this paper
• DNA and the neutral theory.

  1986cited by this paper
• Comparing Multiple Rna Secondary Structures Using Tree Comparisons. a System for Approximate Tree Matching. Ieee Trans. on Knowledge and Data Engineering, in Press. 29 7 Conclusion Extracting Semantic Hierarchies from a Large On- Line Dictionary. I N

  year unknowncited by this paper

• Two new species of Clathrosperchon (Hydrachnidia: Rhynchohydracaridae), and phylogenetic placement of Rhynchohydracaridae

  2024cites this paper
• A New Parasitic Archamoeba Causing Systemic Granulomatous Disease in Goldfish Extends the Diversity of Pathogenic Endolimax spp.

  2023cites this paper
• Molecular phylogenetic assessment of the tribal classification of Lamiinae (Coleoptera: Cerambycidae).

  2020cites this paper
• Molecular phylogeny of Trissolcus wasps (Hymenoptera, Scelionidae) associated with Halyomorpha halys (Hemiptera, Pentatomidae)

  2019cites this paper
• Secondary structure of the internal transcribed rDNA (ITS) regions of Cosmopolites sordidus (Germar) and Odoiporus longicollis (Olivier): a first report in family Curculionidae

  2019cites this paper
• Secondary structure of the internal transcribed rDNA (ITS) regions of Cosmopolites sordidus (Germar) and Odoiporus longicollis (Olivier): a first report in family Curculionidae

  2019cites this paper
• Multiple Sequence Alignment is not a Solved Problem

  2018cites this paper
• Molecular phylogeny of marine mites (Acariformes: Halacaridae), the oldest radiation of extant secondarily marine animals.

  2018cites this paper
• Sequence complementarity at the ribosomal Peptidyl Transferase Centre implies self‐replicating origin

  2017cites this paper
• Size-variable zone in V3 region of 16S rRNA

  2017cites this paper
• Call variation and vocalizations of the stealthy litter frog Ischnocnema abdita (Anura: Brachycephalidae)

  2017cites this paper
• A molecular phylogeny and classification of Anisoptera (Odonata)

  2015cites this paper
• Origin and higher-level diversification of acariform mites – evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment

  2015cites this paper
• Is Sequence Alignment an Art or a Science?

  2015cites this paper
• Sensitivity of Ribosomal RNA Character Sampling in the Phylogeny of Rhabditida.

  2015cites this paper
• Phylogeny and Niche Conservatism in North and Central American Triatomine Bugs (Hemiptera: Reduviidae: Triatominae), Vectors of Chagas' Disease

  2014cites this paper
• Evolution of the ribosome at atomic resolution

  2014cites this paper
• Molecular phylogeny of telenomine egg parasitoids (Hymenoptera: Platygastridae s.l.: Telenominae): evolution of host shifts and implications for classification

  2014cites this paper
• Equivalent Indels – Ambiguous Functional Classes and Redundancy in Databases

  2013cites this paper
• Divergence estimates and early evolutionary history of Figitidae (Hymenoptera: Cynipoidea)

  2012cites this paper
• Phylogeny of fish-infecting Calyptospora species (Apicomplexa: Eimeriorina)

  2012cites this paper
• Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea), based on multiple nuclear genes, and implications for classification

  2011cites this paper
• The First Molecular Phylogeny of Strepsiptera (Insecta) Reveals an Early Burst of Molecular Evolution Correlated with the Transition to Endoparasitism

  2011cites this paper
• Cryptic diversity and female host specificity in a parasitoid where the sexes utilize hosts from separate orders

  2011cites this paper
• Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea), based on multiple nuclear genes, and implications for classification

  2011influential citation
• Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

  2011cites this paper
• DNA barcoding to support conservation: species identification, genetic structure and biogeography of fishes in the Murray)Darling River Basin, Australia

  2011cites this paper
• Systematic revision, cladistics and biogeography of the genus Neogutierrezia Martínez (Coleoptera : Scarabaeidae) and its phylogenetic placement in Rutelinae based on structural alignment of 28S rDNA sequences.

  2010cites this paper
• Defining the genus Hydropsyche (Trichoptera:Hydropsychidae) based on DNA and morphological evidence

  2010cites this paper
• Phylogeny of Gammaproteobacteria

  2010cites this paper
• Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence

  2010influential citation
• Inference of molecular homology and sequence alignment by direct optimization.

  2010cites this paper
• Origin of Clothing Lice Indicates Early Clothing Use by Anatomically Modern Humans in Africa

  2010cites this paper
• A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution.

  2010cites this paper
• Mitochondrial and nuclear markers support the monophyly of Dolichopodidae and suggest a rapid origin of the subfamilies (Diptera: Empidoidea)

  2010cites this paper
• Molecular phylogeny of acariform mites (Acari, Arachnida): strong conflict between phylogenetic signal and long-branch attraction artifacts.

  2010cites this paper
• A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion.

  2009cites this paper
• Comparative analysis of sequences and secondary structures of the rRNA internal transcribed spacer 2 (ITS2) in pollen beetles of the subfamily Meligethinae (Coleoptera, Nitidulidae): potential use of slippage-derived sequences in molecular systematics.

  2009cites this paper
• Molecular phylogeny of the tribe Sphodrini (Coleoptera: Carabidae) based on mitochondrial and nuclear markers.

  2009cites this paper
• Description, circumscription and phylogenetics of the new tribe Zaeucoilini (Hymenoptera: Figitidae: Eucoilinae), including a description of a new genus

  2009cites this paper
• Investigation of distal repetitive sequences in the genus allium

  2009cites this paper
• HYMENOPTERAN MOLECULAR PHYLOGENETICS: FROM APOCRITA TO BRACONIDAE (ICHNEUMONOIDEA)

  2009cites this paper
• Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data

  2009influential citation
• Biogeography and genetic variation of triatomine chagas disease vectors and trypanosoma cruzi isolates from texas

  2009influential citation
• Multigene analysis of phylogenetic relationships and divergence times of primate sucking lice (Phthiraptera: Anoplura).

  2009influential citation
• Structural alignment of 18S and 28S rDNA sequences provides insights into phylogeny of Phytophaga (Coleoptera: Curculionoidea and Chrysomeloidea)

  2009influential citation
• The mitochondrial genome of the 'twisted-wing parasite' Mengenilla australiensis (Insecta, Strepsiptera): a comparative study

  2009cites this paper
• Comparative study of the evolution of nuclear ribosomal spacers incorporating secondary structure analyzes within Dodonaeoideae, Hippocastanoideae and Xanthoceroideae (Sapindaceae).

  2009cites this paper
• A framework for phylogenetic sequence alignment

  2009influential citation
• Laying the foundations for a new classification of Agaonidae (Hymenoptera: Chalcidoidea), a multilocus phylogenetic approach

  2009cites this paper
• What's in a name: the taxonomic status of human head and body lice.

  2008influential citation
• Molecular phylogeny and historical biogeography of the cosmopolitan parasitic wasp subfamily Doryctinae (Hymenoptera:Braconidae)

  2008cites this paper
• Molecular phylogeny of rootworms and related galerucine beetles (Coleoptera: Chrysomelidae)

  2008cites this paper
• Evolution of the parasitic wasp subfamily Rogadinae (Braconidae): phylogeny and evolution of lepidopteran host ranges and mummy characteristics

  2008influential citation
• Relationships Among Species of Scirtothrips (Thysanoptera: Thripidae, Thripinae) Using Molecular and Morphological Data

  2008cites this paper
• A protocol for large-scale rRNA sequence analysis: towards a detailed phylogeny of Coleoptera.

  2008cites this paper
• Phylogenetic Affinities of the Rare and Enigmatic Limb-Reduced Anelytropsis (Reptilia: Squamata) as Inferred with Mitochondrial 16S rRNA Sequence Data

  2008cites this paper
• Phylogeny and evolutionary history of Sapindaceae and Dodonaea

  2008cites this paper
• Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae)

  2007cites this paper
• The secondary structure of the unusually long 18S ribosomal RNA of the myxozoan Sphaerospora truttae and structural evolutionary trends in the Myxozoa.

  2007cites this paper
• Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus).

  2007cites this paper
• The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea)

  2007cites this paper
• Phylogeny of the platygastroid wasps (Hymenoptera) based on sequences from the 18S rRNA, 28S rRNA and cytochrome oxidase I genes: implications for the evolution of the ovipositor system and host relationships

  2007cites this paper
• The impact of length‐variable data and alignment criterion on the phylogeny of Decapodiformes (Mollusca: Cephalopoda)

  2007cites this paper
• A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision

  2007cites this paper
• A molecular phylogeny of the Trichogrammatidae (Hymenoptera: Chalcidoidea), with an evaluation of the utility of their male genitalia for higher level classification

  2007influential citation
• Structural and Evolutionary Considerations for Multiple Sequence Alignment of RNA , and the Challenges for Algorithms That Ignore Them

  2007influential citation
• Phylogeny of parasitiform mites (Acari) based on rRNA.

  2007influential citation
• Multigene phylogeny reveals eusociality evolved twice in vespid wasps

  2007cites this paper
• Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment.

  2007cites this paper
• A single origin of gall association in a group of parasitic wasps with disparate morphologies.

  2007cites this paper
• Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers.

  2006cites this paper
• An evaluation of ensign wasp classification (Hymenoptera: Evaniidae) based on molecular data and insights from ribosomal RNA secondary structure

  2006cites this paper
• Multiple sequence alignment for phylogenetic purposes

  2006cites this paper
• Nematode small subunit phylogeny correlates with alignment parameters.

  2006cites this paper
• Systematics of the cyclostome subfamilies of braconid parasitic wasps (Hymenoptera: Ichneumonoidea): a simultaneous molecular and morphological Bayesian approach.

  2006cites this paper
• Relationships of Exodontiella, a non‐alysiine, exodont member of the family Braconidae (Insecta, Hymenoptera)

  2006influential citation
• Structural homology in ribosomal RNA, and a deliberation on POY

  2006cites this paper
• A secondary structural model of the 28S rRNA expansion segments D2 and D3 for Chalcidoid wasps (Hymenoptera: Chalcidoidea).

  2005cites this paper
• Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules

  2005influential citation
• Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation

  2005cites this paper
• Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted‐wing parasites (Insecta: Strepsiptera)

  2005cites this paper
• A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae)

  2004cites this paper