Simulation tools

This is the page linked in our genome alignment simulation paper.

It is the primary point of access for the three tools described in that paper:

• GSIMULATOR: transducer-based simulation of neutral DNA
• SIMGRAM: simulation from generic phylo-grammars
• SIMGENOME: simulations of structured genomic DNA

Related links:

• simgenome.eg: the underlying grammar of simgenome. Edit to add your own features
  • xrate format: the page documentating the format of this grammar file
• XRATE: the program for estimating parameters of phylo-grammars
• TwelveFlyRocCurveEstimation: details of the benchmarking procedure for generating ROC curves