OmegaPlus / github detects selective sweeps based on the Linkage Disequilibrium signatures.
SweeDgihub
detects selective sweeps using the Site Frequency Spectrum signature
RAiSD github
It combines all 3 known signatures of selective sweeps using the notion of SNP vectors.
Software for simulations
CoMuS / github link
It simulates polymorphic data in a multi-species coalescent framework.
trajdemog
Part of the code was made available from RR Hudson. In fact, I just added some code for simulating data in various demographic models.
SPS / github link
A forward-backward simulator for simulating genetic data in a spatial framework
FEG / github link
An evolutionary game simulator for genetic data. Behavior is under selection pressure. There are “competitors”, “synergists” and individuals who just ignore other members.