We have developed a new computer program (spatpg) to infer variance effective population size and environment-dependent selection based on genetic time-series data (allele frequencies) from multiple populations. The software, including the source code and manual, can be downloaded here or using the link on our software page. The paper describing the method will be published in a forthcoming special issue in Molecular Ecology on detecting selection in natural populations. The accepted article is available here: Gompert-2015-Molecular_Ecology. We hope to release an updated version of the program that supports parallel processing and low-coverage DNA sequenced data shortly.
New software and paper