Sim Gram

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SimGram is a simulator for the XRATE program. It generates randomized sample alignments from a phylo grammar.


SimGram is included with the DART package. See downloading DART for installation instructions.

Example usage

Example usage with the three-state protein secondary structure phylo-HMM of Thorne et al.: Combining protein evolution and secondary structure. Mol. Biol. Evol. 1996;13:666-73.:

 -t tmp/gsimulator-tree.newick
 -g dart/grammars/

Related software

The XRATE tool shares the same grammar file format as SimGram, and can be used to estimate model parameters, or for reconstruction of ancestral sequence. See Xrate Software#simgram

The Sim Genome program is a simulator of multi-genome alignments, built using SimGram and GSIMULATOR.

-- Ian Holmes - 13 Apr 2008