MEGASAT
MEGASAT is a software tool that can automatically infer genotypes from high-throughput microsatellite sequences. MEGASAT is written in Perl & R and includes a simple graphical user interface for Windows and Mac OS X systems.
Installation
Download the whole compressed zip file or just the folder that contains the scripts for your operating system.
If you want to test MEGASAT, you can also download "Megasat_data" that contains FASTQ files for estimating the genotyping error rate and "primer-input.txt" (a text file that contains information of PCR primers, flanking regions and repeated motifs for all the loci).
How to run MEGASAT
The documentation of MEGASAT is the file "MEGASAT Documentation.pdf".