The TKF Structure Tree

The TKF Structure Tree (TKFST) is a continuous-time Markov chain model for evolution of RNA structure, with loops, stems, insertions and deletions, that is based on mutually nested instances of the TKF model.

That is, it is a recursively-nested birth-death process for the evolution of foldback secondary structure in nucleic acid sequences.

TKFST is described in the following open-access paper:

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

Implementations

The TKFST model is implemented by the following programs:

• Evol Sayer, Evol Doer, Indie Gram

In particular, Evol Sayer is a simulation of TKFST on a phylogeny, generating a multiple alignment of RNA sequences, with indels.

Several Phylo Grammar implementations (PFOLD, Evo Fold, XFOLD...) are close approximations or relations to the TKF structure tree, with less-rigorous indel modeling.

-- IanHolmes - 08 Aug 2008