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 (1996):

• 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 XrateSoftware#simgram

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

-- IanHolmes - 13 Apr 2008