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Comparison of the Verlet table and cell-linked list algorithms for sequential, vectorized and multithreaded implementations" . Fomin E.S. Neighbor search algorithms are widely used in molecular dynamics for the direct computation of short-range inter-atomic potentials. These algorithms are based on the Verlet table (VT) or cell-linked list (CLL) methods. ... Keywords: Verlet table method, cell-linked list method, nearest neighbor search, SIMD, multithreading . ...

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... Instructions are in README.TXT file inside the tarball. ... tar -xvf nhunt_x86.tar Query and database files should contain sequences in FASTA format ( wikipedia description ). ... Default name of the output file is 'nhunt.out'. ... Any parameter consists of key and value and is called as '-key value', where 'key' is one character and 'value' is any number of characters. -i Query file . ... No default value. -d Database file . ... No default value. -o Output file . ... Default value: 'nhunt.out' . ...

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• Comparison of protein phylogeny reconstruction methods

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