treesimj

TreesimJ is a forward-time simulator of an evolving population that tracks the evolutionary tree of the entire population. The application offers an intuitive GUI, a variety of pre-configured models of fitness, mutation, and demography, and a suite of data collectors that analyze the population and emit data to one or more sources. To the user, TreesimJ offers a simple, easy to use interface, a variety of interchangeable "models" describing many aspects of the evolving population, and many ways to quantify and summarize the state of the population. Since the entire tree of the population is tracked, TreesimJ can easily be used to asses the average time to most recent common ancestor, the level of tree imbalance, or the mean pairwise coalescent time. It can also compute a number of familiar population genetic statistics, such as the nucleotide diversity and the number of segregating sites (if a model of fitness that includes DNA is used). The list of potential data collecting items i