Software

The SSW simulation and CLSW analysis package of Kim & Stephan (2002), as well as the GOF analysis package of Jensen et al. (2005). (code written by Yuseob Kim). clsw

The omega_max LD calculator of Jensen et al. (2007). (code written by Kevin Thornton). omega

The simulation code for simulating a sweep in a bottlenecked population (plus the ancestral population) of Thornton & Jensen (2007). (code written by Kevin Thornton). bneck+HH_simcode

The simulation code for models of recurrent hitchhiking of Jensen et al. (2008). (code written by Kevin Thornton). RHH_simcode

The ABC package used in Jensen et al. (2008). (code written by Kevin Thornton). ABC

The joint omega / Sweepfinder analysis of Pavlidis et al. (2010). (code written by Pavlos Pavlidis). omega_split; omega_sweepfinder

The time-sampled selection analysis (WFABC) software of Foll et al. (2014) and Foll et al. (2015). (code written by Matthieu Foll). WFABC_v1.1

PopPlanner is a GUI program to interactively construct ms and msms command lines as described in Ewing & Jensen (2015), here as an executable jar file. (code written by Greg Ewing). PopPlanner.jar

The ABC package for estimating beneficial allele age as described in Ormond et al. (2016). (code written by Louise Ormond). ABC_inference; testdata

The CP-WFABC software for time-sampled selection analysis of Shim et al. (2016). (code written by Hyunjin Shim). CPWFABC_v1.0

TEMPLEv1.0: A program for analyzing intraspecific genetic diversity at transcription factor binding sites (developed by Maria Litovchenko and Stefan Laurent). temple_v1-4-2.0