Evol Deeds

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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)
  • Color Stock, a command-line visualization tool for colorizing RNA alignments

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

Authors

Availability

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

-- Ian Holmes - 09 Dec 2008