Koetschan et al. (2010) NAR 38:D275-9
Selig et al. (2008) NAR 36:D377-380.
Schultz et al. (2006) NAR 34:W704-7.
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ITS2 3D structure
(Keller et al. 2010)


Chlorophyta hypertree

(Buchheim et al. 2011)
Fig1, Fig2, Fig3, Fig4

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RNA movie for a scenedesmacean ITS2

  • 4SALE
    A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing
  • ATV
    Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Trees
  • CBCanalyzer
    Inferring phylogenies based on compensatory base changes in rRNA secondary structures
  • Clustal
    Multiple alignment of nucleic acid and protein sequences
  • FigTree
    FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures
  • HMMER
    HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis
  • HyperGeny
    HYPERbolic phyloGENY viewer allows hyperbolic visualisation of very large tree structures. Both an online and offline version is available
  • lara
    lara ("lagrangian relaxed structural alignment") is a tool for the sequence-structure alignment of RNA sequences
  • Locomotif
    Locomotif is a GUI-based program that allows for the visual design of RNA motifs
  • Marna
    Multiple alignment of RNAs taking into consideration both the primary and the secondary structure
  • MEME
    MEME is a tool for discovering motifs in a group of related DNA or protein sequences
  • Mfold
    RNA & DNA Folding Application
  • NCBI
    National Center for Biotechnology Information
  • ProfDistS
    (Profile-) Distance based phylogeny on sequence-structure alignments
  • Pseudoviewer
    Visualization of RNA pseudoknots of any type
  • RNA2D3D
    An interactive system for the conversion of RNA 2D structures to 3D and 3D modeling.
  • RNAforester
    Calculate pairwise global structural alignments
  • RNAMovies
    Sequential Animation of RNA secondary structure including pseudoknots and entangled helices
  • RNAstructure
    RNA secondary structure prediction and analysis software
  • RNA Structure Logo
    The structure logo is an extension of the sequence logo
  • SISSI
    SISSI is a software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices
  • UNAFold
    UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction
  • Vienna RNA Package
    RNA Secondary Structure Prediction and Comparison
  • WebLogo
    WebLogo is a web based application designed to make the generation of sequence logos

Applications / Journals

Applications / Journals

If you use the database please cite.