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WindowMasker: Installed on HPC
WindowMasker is a denovo repeat finder from the NCBI, published in 2006, A denovo repeat finder is a program designed to find repeats in DNA sequence without using the RepeatMasker. RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by the program cross_match, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green.
More information on WindowMasker; http://genomewiki.ucsc.edu/index.php/WindowMasker
http://bioinformatics.oxfordjournals.org/cgi/content/full/22/2/134
Installation: