SINCOPA
https://sincopa.tau.ac.il/ 
Detecting selective sweeps in bacteria based on Similarity of INCOngruent PAtterns
The SINCOPA algorithm is the first ever phylogeny-based algorithm for paritial and soft selective sweeps detection that is tailored for bacterial data. SINCOPA is based on detecting similarity of incongruent allelic patterns in a given DNA multiple sequence alignment. SINCOPA is freely available to use through SINCOPA web server. For further details see SINCOPA's overview page.