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 recursively 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 papers:

• Holmes I.  A probabilistic model for the evolution of RNA structure.  BMC Bioinformatics. 2004 Oct 26;5:166.
• Bradley RK, Holmes I.  Evolutionary triplet models of structured RNA.  PLoS Comput Biol. 2009 Aug;5(8):e1000483. Epub 2009 Aug 28.

Implementations

The TKFST model is implemented by the following programs:

• Evol Sayer - a simulation of TKFST on a phylogeny, generating a multiple alignment of RNA sequences, with indels.
• Evol Doer - pairwise alignment using TKFST. Can also export the TKFST pair SCFG in Stem Loc grammar format
• Indie Gram - triplet alignment using TKFST

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