SimGenome

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

It can also use other simulation tools as plug-in "feature generators".

Installation

Installation instructions:

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

Once installed, run the script dart/perl/simgenome.pl

You can also browse the underlying grammar: 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

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

-- IanHolmes - 13 Apr 2008