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 &: A probabilistic model for the evolution of RNA structure. BMC Bioinformatics 2004;5:166.
- Bradley & Holmes: Evolutionary triplet models of structured RNA. PLoS Comput. Biol. 2009;5:e1000483.
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
-- Ian Holmes - 08 Aug 2008