optiFLP: software for automated optimization of amplified fragment length polymorphism scoring parameters

Mol Ecol Resour. 2011 Nov;11(6):1113-8. doi: 10.1111/j.1755-0998.2011.03043.x. Epub 2011 Jun 28.


Amplified fragment length polymorphism (AFLP), a widely used method for DNA fingerprinting, has shifted from polyacrylamide gel to capillary electrophoresis over the last years. Currently, most AFLP data are generated in a computer-readable format, and several programs are available that automatically score raw data into binary profiles. Good scoring parameters are the key to good AFLP profiles. optiFLP is the first open source program for automatic optimization of AFLP scoring parameters. It searches parameter space to maximize the contrast among groups of AFLP profiles, with the allocation of profiles to groups in either a supervised or an unsupervised mode. The software produces output files ready for use in a range of downstream applications.

MeSH terms

  • Algorithms*
  • Amplified Fragment Length Polymorphism Analysis / methods*
  • DNA Fingerprinting / methods*
  • Models, Genetic*
  • Software*