DTscore is a distance based tamdem duplication tree reconstruction algorithm. It is based on a simple tandem duplication model, which assumes unequal recombination (crossover) as the only duplication mechanism. All it takes as input is a distance matrix between copies. In this matrix, the rows and columns need to be ordered in the same way as the copies are ordered on the locus. DTscore can be applied to relatively large datasets (more than a hundred copies). Distances can be calculated using programs such as DNADIST (nucleotide sequences) or PROTDIST (protein sequences) from the PHYLIP package. Heterogeneous rates of substitution among sites can be dealt with using the GAMMA method, for example.
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Elemento O. and Gascuel O.
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees.
Bioinformatics. 2002 18 :S92-S99.