dadi (Diffusion Approximations for Demographic Inference)
Rapid and powerful diffusion method for fitting models of demographic history and selection to genetic polymorphism data.
dadi-cli
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Powerful and convenient command-line interface for using dadi, including parallel and distributed computing.
donni (Demographic Optimization via Neural Network Inference)
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Instantaneously infer models of demographic history from allele frequency spectra using pre-trained neural networks.
batcaver
Improve identification of somatic tumor mutations by Mutect, by incorporating information about individual tumor mutation profiles.
SloppyCell
SBML-compatible environment for building, fitting, and analyzing biochemical models, with an emphasis on parameter sensitivity.