Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules. (Q52653070)

5 May 2018

title

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

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5 May 2018

author name string

Joseph J Gillespie

series ordinal

1

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5 May 2018

publication date

1 December 2004

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5 May 2018

Molecular Phylogenetics and Evolution

published in

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5 May 2018

volume

33

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5 May 2018

issue

3

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5 May 2018

page(s)

936-943

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5 May 2018

The its Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny

cites work

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Cirripede phylogeny using a novel approach: molecular morphometrics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Crayfish Molecular Systematics: Using a Combination of Procedures to Estimate Phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Sequence and secondary structure variation in the Gyrodactylus (Platyhelminthes: Monogenea) ribosomal RNA gene array

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Evolution according to large ribosomal subunit RNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Molecular evolution of the mitochondrial 12S rRNA in Ungulata (mammalia).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Convergent evolution of cucurbitacin feeding in spatially isolated rootworm taxa (Coleoptera: Chrysomelidae; Galerucinae, Luperini).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

How Slippage-Derived Sequences Are Incorporated into rRNA Variable-Region Secondary Structure: Implications for Phylogeny Reconstruction

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

RNA secondary structure: physical and computational aspects

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Ribosomal DNA: Molecular Evolution and Phylogenetic Inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Fast folding and comparison of RNA secondary structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Secondary structural and phylogenetic implications of nuclear large subunit ribosomal RNA in the ectomycorrhizal fungus Tricholoma matsutake

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Molecular phylogenetics at the Felsenstein zone: approaching the Strepsiptera problem using 5.8S and 28S rDNA sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

DNA and the neutral theory

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Mosquito large subunit ribosomal RNA: simultaneous alignment of primary and secondary structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Phylogeny of Trichoptera (caddisflies): characterization of signal and noise within multiple datasets

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Internal Transcribed Spacer Sequences from 38 Recognized Species of Suillus sensu lato: Phylogenetic and Taxonomic Implications

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Systematics of Nothofagus (Nothofagaceae) based on rDNA spacer sequences (ITS): taxonomic congruence with morphology and plastid sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

A probabilistic treatment of phylogeny and sequence alignment.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Molecular systematics of hystricognath rodents: evidence from the mitochondrial 12S rRNA gene

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

RAGA: RNA sequence alignment by genetic algorithm

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

18S rRNA Secondary Structure and Phylogenetic Position of Peloridiidae (Insecta, Hemiptera)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Louse (Insecta: Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Estimating the contributions of selection and self-organization in RNA secondary structure.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Molecular homology assessment and phylogeny in the lizard family opluridae (Squamata: Iguania).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Comparison of the nucleotide sequence and secondary structure of the 5.8S ribosomal RNA gene of Chlamydomonas tetragama with those of green algae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

18S ribosomal RNA and tetrapod phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.YMPEV.2004.08.004

10.1016/J.YMPEV.2004.08.004

7 January 2021

Identifiers

DOI

1 reference

5 May 2018

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5 May 2018