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optiFLP: software for automated optimization of amplified fragment length polymorphism scoring parameters
Author(s) -
ARTHOFER W.,
SCHLICKSTEINER B. C.,
STEINER F. M.
Publication year - 2011
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/j.1755-0998.2011.03043.x
Subject(s) - biology , fragment (logic) , software , amplified fragment length polymorphism , genetics , computational biology , polymorphism (computer science) , genotype , algorithm , programming language , computer science , gene , population , demography , sociology , genetic diversity
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.