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 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.:
- Input tree file: simgram-tree.newick (Newick Format)
- Input grammar file: prot3.eg (Xrate Format)
- Output alignment file: simgram-output.stock (Stockholm Format)
./dart/bin/simgram -t tmp/gsimulator-tree.newick -g dart/grammars/prot3.eg >tmp/gsimulator-output.stock
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