HomologMiner is a software to identify homologous groups applicable to genome sequences that have been properly marked for low-complexity repeats and annotated interspersed repeats.
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Bioinformatics. 2007 Apr 15;23(8):917-25. Epub 2007 Feb 18.
HomologMiner: looking for homologous genomic groups in whole genomes.
Hou M, Berman P, Hsu CH, Harris RS.