SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.
NetworkX is a Python language software package for the creation, manipulation, and study of the structure, dynamics, and function of complex networks.
GNU Octave mathematics-oriented syntax with built-in plotting and visualization tools.
IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program’s basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.
ITensor—Intelligent Tensor—is a C++ library for implementing tensor network calculations.
The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the ‘query’ files), when compared with a reference annotation (also provided as GFF).
