Evol Deeds

The EvolDeeds package simulates the evolution of RNA structure both forwards and backwards in time, by probabilistic means.

It includes the following packages:

• EvolSayer, a forward-time simulator
• EvolDoer (formerly 'tkfstalign'), a pairwise aligner
• IndieGram, a code-generating three-way aligner & ancestral reconstructor

Related programs in the DART package include

• StemLoc, a heuristic but extremely accurate RNA multiple alignment tool (configurable pair SCFGs; multiple alignment via sequence annealing or single-linkage clustering)
  • EvolDoer can export pair-SCFGs for the TKF structure tree model in stemloc grammar format
• ColorStock, a command-line visualization tool for colorizing RNA alignments

The EvolDeeds package uses TreeTransducers, specifically the TKF Structure Tree.

Authors

• RobertBradley
• IanHolmes

Availability

Evol Deeds is distributed as part of the DART package for DNA, Amino Acid & RNA Tests.

• DownloadingDART

-- IanHolmes - 09 Dec 2008