(Q51711710)

10 April 2018

title

Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment. (English)

1 reference

10 April 2018

1 reference

Karl M Kjer

1

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10 April 2018

Joseph J Gillespie

series ordinal

2

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10 April 2018

Karen A Ober

series ordinal

3

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10 April 2018

publication date

1 February 2007

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10 April 2018

published in

Systematic Biology

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10 April 2018

volume

56

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10 April 2018

issue

1

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10 April 2018

page(s)

133-146

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10 April 2018

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

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21 January 2018

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21 January 2018

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Influence of alignment on the mtDNA phylogeny of Cetacea: questionable support for a Mysticeti/Physeteroidea clade

21 January 2018

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Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

21 January 2018

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Problems with Parsimony in Sequences of Biased Base Composition

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

A Successive Approximations Approach to Character Weighting

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

Simultaneous statistical multiple alignment and phylogeny reconstruction.

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

A benchmark of multiple sequence alignment programs upon structural RNAs

21 January 2018

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A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods

21 January 2018

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

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera).

21 January 2018

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Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation.

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

A Review of Arthropod Phylogeny: New Data Based on Ribosomal DNA Sequences and Direct Character Optimization

21 January 2018

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21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

Likelihood-based tests of topologies in phylogenetics

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

Finding the most significant common sequence and structure motifs in a set of RNA sequences

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

The accuracy of ribosomal RNA comparative structure models

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

Alignment of RNA base pairing probability matrices

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

A probabilistic model for the evolution of RNA structure

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

Aligned 18S and insect phylogeny.

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

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https://api.crossref.org/works/10.1080%2F10635150601156305

Bayesian coestimation of phylogeny and sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

A "Long Indel" model for evolutionary sequence alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Comparative analysis of mt LSU rRNA secondary structures of Odonates: structural variability and phylogenetic signal

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

A probabilistic treatment of phylogeny and sequence alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

A general method applicable to the search for similarities in the amino acid sequence of two proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

RNA structure: reading the ribosome

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

T-Coffee: A novel method for fast and accurate multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

RAGA: RNA sequence alignment by genetic algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Finding the common structure shared by two homologous RNAs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Multiple sequence alignment in phylogenetic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Joint Bayesian Estimation of Alignment and Phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

MrBayes 3: Bayesian phylogenetic inference under mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

A Stochastic Model for the Evolution of Autocorrelated DNA Sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Sequence alignment of 18S ribosomal RNA and the basal relationships of Adephagan beetles: evidence for monophyly of aquatic families and the placement of Trachypachidae

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Independence of alignment and tree search.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Multiple sequence alignment with the Divide-and-Conquer method

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

An evolutionary model for maximum likelihood alignment of DNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Database on the structure of small subunit ribosomal RNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Sequence alignment and penalty choice. Review of concepts, case studies and implications

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Search-based optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

The Phylogeny of the Extant Hexapod Orders

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata: Scincidae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Structure of the 30S ribosomal subunit

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

18S ribosomal RNA and tetrapod phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

Mfold web server for nucleic acid folding and hybridization prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

On the Correlation Between Composition and Site-Specific Evolutionary Rate: Implications for Phylogenetic Inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150601156305

10.1080/10635150601156305

21 January 2018

Identifiers

DOI

1 reference

10 April 2018

release_36nv47pdkngotnime5z37frjp4

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/36nv47pdkngotnime5z37frjp4

mapped directly with Wikidata item

24 November 2022

based on heuristic

PubMed ID

17366144

1 reference

10 April 2018