Evol Deeds

Evol Deeds

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

It includes the following packages:

• Evol Sayer, a forward-time simulator
• Evol Doer (formerly 'tkfstalign'), a pairwise aligner
• Indie Gram, a code-generating three-way aligner & ancestral reconstructor

Related programs in the DART package include

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

The Evol Deeds package uses Tree Transducers, specifically the TKF Structure Tree.

Authors

• Robert Bradley
• Ian Holmes

Availability

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

• Downloading DART

-- Ian Holmes - 09 Dec 2008