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RNAalishapes
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RNAalishapes is a tool for secondary structure prediction, using shape abstraction. Input is a multiple sequence alignment. Pseudoknots are not considered at all.
The image below shows the analysis of tRNA sequences.

A previous version from the original author Björn Voß can be found here.

Author: S. Janssen

Users of RNAalishapes are requested to cite :
Janssen, Stefan and Giegerich, Robert The RNA shapes studio, Bioinformatics, 2015