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FFTW++ is a C++ header class for the FFTW Fast Fourier Transform library that automates memory allocation, alignment, planning, wisdom, and communication on both serial and parallel (OpenMP/MPI) architectures. In 2D and 3D, hybrid dealiasing of convolutions substantially reduces memoryusage and computation time. Wrappers for C, Python, and Fortran are included.
...Lybanon and "Fast additions on masked integers" by Michael D. Adams and David S. Wise.
On 2009's computers it works quite well up to graph sizes of about 28 nodes. Runtime and memoryusage are exponential in the graph size.
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.
Judy is a general purpose dynamic array implemented as a C callable library. Judy's speed and memoryusage are typically better than other data storage models and improves with very large data sets.
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