We introduce the software tool NTRFinder to search for a complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that NTRs can be used as phylogenetic and population markers. We have tested our algorithm on both real and simulated data, and present some real NTRs of interest. NTRFinder can be downloaded from http://www.maths.otago.ac.nz/~aamatroud/

A. A. Matroud

C. P. Tuffley

Domanic

Hauth

Landau

M. D. Hendy

Matroud

Sagot

Wells

Wexler

Woodford

Crossref

PubMed Central

Nucleic Acids Research

English

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