Simulation Tools

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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
  • Twelve Fly Roc Curve Estimation: details of the benchmarking procedure for generating ROC curves