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; ABC_inference_non_equilibrium;  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

The MMC analysis of Matuszewski et al. (2018). (code written by Sebastian Matuszewski). github

The MMC-ABC package of Sackman et al. (2019). (code written by Andrew Sackman). github

The ABC package and analysis scripts for jointly inferring population size change with the DFE of Johri et al. (2020). (code written by Parul Johri). github

The code and analysis scripts related to the effects of background selection on demographic inference of Johri et al. (2021). (code written by Parul Johri). github

The code and analysis scripts related to deleterious fixations of Johri, Charlesworth, et al. (2021). (code written by Parul Johri). github

The code and analysis scripts related to bacterial recombination rate estimation of Sabin et al. (2022). (code written by Susanna Sabin). github

The code and analysis scripts related to DFE inference in viruses of Morales-Arce, Johri, et al. (2022). (code written by Ana Morales-Arce and Parul Johri). github

The code and analysis scripts related to soft selective sweeps of Johri et al. (2022a). (code written by Parul Johri). github

The code and analysis scripts related to our Perspective on population genomic inference of Johri et al. (2022b). (code written by Parul Johri). github

The code and analysis scripts related to a human-specific evolutionary baseline model of Johri et al. (2023). (code written by Parul Johri). github

The code and analysis scripts related to recurrent selective sweeps of Soni et al. (2023). (code written by Viv Soni). github

The code and analysis scripts related to the simulation of within-patient SARS-CoV-2 data of Terbot et al. (2023). (code written by John Terbot II). github

The code and analysis scripts related to mutation and recombination rate heterogeneity of Soni et al. (2024). (code written by Viv Soni). github

The code and analysis scripts related to the detection of selection in SARS-CoV-2 of Soni, Terbot, & Jensen (2024). (code written by Viv Soni and John Terbot II). github

The code and analysis scripts related to the detection of balancing selection of Soni & Jensen (2024). (code written by Viv Soni). github