batcaver
Improve identification of somatic tumor mutations by Mutect, by incorporating information about individual tumor mutation profiles.
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.
SloppyCell
SBML-compatible environment for building, fitting, and analyzing biochemical models, with an emphasis on parameter sensitivity.