LadderFinder is a GPL program designed to solve a problem in DNA genotyping. It helps in the construction of allelic ladders that drive the sizing and binning of SSR fragments produced by PCR. The algorithm scans a spreadsheet containing a database of individual profiles and finds a minimum set of individuals, that covers the maximum number of alleles represented in the database, with all alleles represented only once. The last constraint is imposed to make homogeneous the ladder peaks in the pherograms. Given such a constrain, the best solution may not include all alleles.

LadderFinder consists of two components: a graphical interface and a program kernel.
The graphical interface is written in JAVA be portable, while the program kernel, called matchfinder, is written in C++ for efficency porpouse.

The graphical interface uses both JExcel and Swing-Layout and it allows to load an Excel/OpenOffice spreadsheet representing allele lengths for each couple species/microsattelite.