MicroFamily is a program designed for identifying flanking region similarities between different microsatellite sequences obtained from screening partial genomic libraries.
GenoTan is a free tool to identify length variation of microsatellites from short sequence reads. Inferring lengths of inherited microsatellite alleles with single base pair resolution from short sequence reads is challenging due to several sources of noise including PCR amplification errors, individual cell mutation, misalignment or mis-mapping caused by the repetitive nature of the microsatellites. We have developed a method using a discretized Gaussian mixture model combined with a rules-based approach to identify inherited variation of microsatellite loci from short sequence reads, which effectively distinguishes length variants from INDEL errors at homopolymers.