LZW-Kernel

Implementation of the LZW-Kernel function for biological sequences.

For more information see: Reference: Authors: Gleb Filatov, Bruno Bauwens, Attila Kert'esz-Farkas Title: LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification email: akerteszfarkas@hse.ru

Install:

$ make

Usage:

For LZW-Kernel use:
$ lzw-kernel_all_vs_all input_sequences.fasta > sequnces.kernel_mx

For LZW-NCD use:
$ lzw-dist_all_vs_all input_sequences.fasta > sequnces.dist_mx

Example:

$ lzw-kernel_all_vs_all test.fasta > test.kernel_mx