  We introduce the software tool NTRFinder to find the 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 nested tandem repeats can be used as phylogenetic and population markers.
We have tested our algorithm on both real and simulated data, and present some
real nested tandem repeats of interest. We discuss how the NTR found in the
ribosomal DNA of taro (Colocasia esculenta) may assist in determining the
cultivation prehistory of this ancient staple food crop. NTRFinder can be
downloaded from http://www.maths.otago.ac.nz/? aamatroud/.
