Freiburg RNA Tools
LocARNA - Alignment & Folding
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LocARNA

LocARNA - Alignment & Folding

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

Try LocARNA with these examples:

Sequence and Structure

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When using LocARNA please cite :

Results are computed with LocARNA version 1.8.11 linking Vienna RNA package 2.2.8