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EAGLE: alignment-free method to compute relative absent words (RAWs)
EAGLE is an alignment-free method and associated program to compute relative absent words (RAW) in genomic sequences using a reference sequence. Currently, EAGLE runs on a command line linux environment, building an image with patterns reporting the absent words regions (in SVG) as well as reporting the associated positions into a file. EAGLE has got scripts to run on the current outbreak and the other existing ebola virus genomes (using the human as a reference), including the download, filtering and processing of the entire data.
Raquel M. Silva, Diogo Pratas, Luísa Castro, Armando J. Pinho & Paulo J. S. G. Ferreira. Bioinformatics (2015): btv189.