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Generate mutated sequence files from a reference genome.

Project Description

Generate mutated sequence files from a reference genome.

SNP Mutator was developed by the United States Food and Drug Administration, Center for Food Safety and Applied Nutrition.


  • Reads a fasta file and generates any number of mutated fasta replicate files.
  • Mutations can be any number of single-base substitutions, insertions, and deletions at randomly chosen positions, uniformly distributed across the genome.
  • Generates a summary file listing the original base and the mutation for all mutated positions.

Citing SNP Mutator

To cite SNP Mutator, please reference the SNP Mutator GitHub repository:


See the LICENSE file included in the SNP Mutator distribution.


0.2.0 (2016-01-15)

  • Allow lowercase bases in the input fasta file.
  • Do not mutate gaps or ambiguous positions.
  • Add a command line switch to show the program version.

0.1.1 (2015-06-17)

  • Remove spaces from the summary file column headings. This will simplify downstream analysis in some scripting languages.

0.1.0 (2015-05-21)

  • First release on GitHub, Read the Docs, and PyPI.

Release History

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Source None Jan 15, 2016

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