GSIMULATOR is a program that uses context-dependent string transducers to simulate genome evolution.
With CVS installed, check out the source code from the CVS repository by typing the following from a terminal prompt:
cvs -d:ext:email@example.com:/usr/local/cvs co gsimulator
The source code may also be browsed here:
Example usage with models trained on human-chimp alignments:
- Input tree file: gsimulator-tree.newick (Newick Format)
- Output alignment file: gsimulator-output.stock (Stockholm Format)
./gsimulator/bin/gsimulator.pl -r ./gsimulator/trained-models/humanChimpChr1_Singlet0.tra -b ./gsimulator/trained-models/humanChimpChr1_Gotoh0.tra tmp/gsimulator-tree.newick >tmp/gsimulator-output.stock
See also SIMGENOME for a related simulator that combines gsimulator with a feature-rich phylo-grammar.