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                                    Bielefeld         University Bioinformatic Service
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RNAforester2

RNAforester2 is a command line based tool for RNA secondary structure comparison. The comparison can be done in a pairwise and multiple alignment fashion and is based on the forest alignment model.

RNAforester2 is an extended version of RNAforester, and allows forest alignment with a linear or an affine gap cost model. For output of the program RNAcast, RNAforester can speed up the alignment computation by anchoring the subalignments based on a common abstract shape.

Users of RNAforester2 at BiBiServ are requested to cite:
Stefanie Schirmer, Robert Giegerich
Forest alignment with affine gaps and anchors
Proceedings of the 22nd Annual Symposium on Combinatorial Pattern Matching, pages 104-107.
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Fri Dec 14 13:00:48 2012