LocARNA is a tool for multiple alignment of RNA molecules. LocARNA requires only RNA sequences as input and will simultaneously fold and align the input sequences. Specifications of additional constraints or fixed input structures are possible. LocARNA outputs a multiple alignment together with a consensus structure. For the folding it makes use of a very realistic energy model for RNAs as it is by RNAfold of the Vienna RNA package (or Zuker's mfold). For the alignment it features RIBOSUM-like similarity scoring and realistic gap cost. The LocARNA software is available for download as part of the LocARNA package (GPL 3).

For articles describing the tool and webserver refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

• Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen.
  LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
  RNA, 18 no. 5, pp. 900-14, 2012
  
• Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen.
  Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering
  PLoS Computational Biology, 3 no. 4, pp. e65, 2007
  
• Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
  Freiburg RNA tools: a central online resource for RNA-focused research and teaching
  Nucleic Acids Research, 46(W1), W25-W29, 2018.