Programs that we make available include
- discoal- a coalescent simulation program capable of simulating models with recombination, migration, selective sweeps, and population size changes. A unique feature is that discoal can generate draws from the coalescent conditional on the fixation of individual sites as a result of a hard sweep, a soft sweep, or drift.
- S/HIC- the Soft Hard Inference tool via Classification. This collection of software tools uses a supervised machine learning approach (i.e. an extra trees classifier) to accurately differentiate regions of the genome that have been affected by hard sweeps and soft sweeps from those genomic locations that are linked to either hard or soft sweeps or are unaffected by linked selection.
- diploS/HIC- our second generation version of S/HIC that is suitable for unphased diploid data. diploS/HIC uses a deep learning, convolutional neural network to perform classification on a novel feature space that provides greater accuracy and robustness over the original S/HIC method.
- IM_CLAM- Isolation with Migration model inference via Composite Likelihood Analysis of Markov chains. This collection of software tools implements the Markov chain method described by Kern and Hey (2016) for exact calculation of the joint allele frequency spectrum from IM models and associated inference.