Peakmatcher: Software for semi-automated fluorescence-based AFLP

Fluorescence-based amplified fragment length polymorphism (AFLP) is becoming a widely used molecular marker technology. The fluorescence-based technique is particularly desirable because it allows for semiautomation of gel scoring. However, semiautomated gel scoring requires manual creation of marker categories, which is time consuming. We have developed Peakmatcher software to create automatically marker categories and generate a binary table for the presence or absence of marker fragments. Peakmatcher generates categories primarily on the basis of the repeatability of markers across replications. The program produces results that are highly consistent with those from a graphical manual method. Furthermore, Peakmatcher required only about 10% as much time to generate comparable data. We conclude that the capability of Peakmatcher to analyze large data sets rapidly will expedite semiautomated fluorescence-based AFLP.