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)
- Color Stock, a command-line visualization tool for colorizing RNA alignments
Evol Deeds is distributed as part of the DART package for DNA, Amino Acid & RNA Tests.
-- Ian Holmes - 09 Dec 2008