BRA (Binary Repeat Align) is a software for aligning tandem repeat regions for which the repeats can be treated as marked by mutations. Tandem repeat regions are abundant in many genomes. Normally not very informative, except for various fingerprinting techniques using length statistics, regions where the repeats are marked, that is, there are slight variations of the basic repeat, remarkable patterns can occur. These patterns can be utilized for evolutionary analysis.
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Savolainen P, Arvestad L, Lundeberg J (2000a) mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats. Mol Biol Evol 17(4), 474—478
Savolainen P, Arvestad L, Lundeberg J (2000b) A novel method for forensic DNA investigations: repeat-type sequence analysis of tandemly repeated mtDNA in domestic dogs. J Forensic Sci 45(5), 990—999