Evol Doer (formerly 'tkfstalign')

Evol Doer is a program for pairwise RNA structural-phylo alignment operations based on the TKF Structure Tree model.

It is part of the Evol Deeds package, which itself is distributed as part of the DART package.

Evol Doer's pair grammars can be viewed as Tree Transducers: combinable machines for analysis of RNA structural alignments.

Reference:

• Holmes I.  A probabilistic model for the evolution of RNA structure.  BMC Bioinformatics. 2004 Oct 26;5:166.