GSimulator

GSIMULATOR is a program that uses context-dependent string transducers to simulate genome evolution.

Installation

With CVS installed, check out the source code from the CVS repository by typing the following from a terminal prompt:

cvs -d:ext:anonymous@cvs.biowiki.org:/usr/local/cvs co gsimulator

The source code may also be browsed here:

• BiowikiCvsDir:gsimulator

Example usage

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

Related software

See also SIMGENOME for a related simulator that combines gsimulator with a feature-rich phylo-grammar.