LocARNA is a collection of alignment tools for the structural analysis of RNA.
Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common
structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment
and is in particular suited for analyzing sets of related RNAs without known
common structure.

LocARNA distinguishes itself from many other Sankoff-style multiple alignment
programs by its performance and low memory complexity, high accuracy, and
richness of features. As unique features, it offers structure-local alignment,
flexible structure and anchor constraints, and provides efficient computation of
reliabilities in sequence-structure alignment. The package offers a robust core
of features and is used as experimental platform for the incorporation of new
features in RNA sequence-structure alignment.

WWW: https://github.com/s-will/LocARNA