Phylogeny and comparative genomics - DT-SCORE
DTscore is a distance based tandem 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.