Sim Genome

SimGenome

SimGenome is a simulator for syntenic genomic blocks, built using SIMGRAM and GSIMULATOR.

Installation

Installation instructions:

1. Install DART (see downloading DART).
2. Install GSIMULATOR.

Once installed, run the script [DartPerl:simgenome.pl dart/perl/simgenome.pl]

You can also browse the underlying grammar: [DartGrammar:simgenome.eg dart/grammar/simgenome.eg]

Example usage

Example usage:

• Input tree file: simgenome-tree.newick (Newick Format)
• Output alignment file: simgenome-output.stock (Stockholm Format)

./dart/bin/simgenome
 tmp/simgenome-tree.newick
 >tmp/simgenome-output.stock

Related software

• Sim Gram -- general simulation tool for phylo grammars
• GSIMULATOR -- simulation of neutral DNA

-- Ian Holmes - 13 Apr 2008