jPopGen Suite is an user-friendly package of java programs for population genetic analysis of SNP spectrum data from randomly sampled DNA sequences. The current version (v1.0b7) provides functions to estimate population parameters (population mutation rate, population exponential growth rate and sequencing error rate) and conduct neutrality tests.
If you use jPopGen Suite, please cite: Liu X. 2012. jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors. Methods in Ecology and Evolution. 3: 624-627.