Sim Gram

SimGram

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

Installation

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.:

• 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

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