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

The omega_max LD calculator of Jensen et al. (2007). omega

The simulation code for simulating a sweep in a bottlenecked population of Thornton & Jensen (2007). bneck+HH_simcode

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

The ABC package used in Jensen et al. (2008). ABC

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

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

PopPlanner is a GUI program to interactively construct ms and msms command lines as described in Ewing & Jensen (2015). PopPlanner.jar

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

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

TEMPLEv1.0: A program for analyzing intraspecific genetic diversity at transcription factor binding sites. temple_v1-4-2.0

The MMC analysis of Matuszewski et al. (2018). github

The MMC-ABC package of Sackman et al. (2019). github

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

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

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

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

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

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

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

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

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

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

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

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

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

Recombination maps for rhesus macaques of Versoza, Weiss, et al. (2024). data

The code and analysis scripts related to the quantification of the demographic history of aye-ayes of Terbot et al. (2025). github

The code and analysis scripts related to 2-step demographic and DFE inference of Soni & Jensen (2025). github

The code and analysis scripts related to CO/NCO detection in aye-ayes of Versoza, Lloret-Villas, et al. (2025). github

The code and analysis scripts related to positive and balancing selection scans in aye-ayes of Soni et al. (2025a). github

The code and analysis scripts related to demographic inference in marmosets of Soni et al. (2025b). github