Maize Xa21 disease resistance genes
The most parsimonious duplication tree (DTEXPLORE) is identical to the most parsimonious phylogeny (DNAPENNY) and requires 2212 parsimony steps. DTSCORE finds the same duplication tree. There are two potential root locations, and we have not tried to estimate wich one is the best one. Associated article (in which the authors present a duplication history which is close but not identical to ours) : Song WY et al. Evolution of the rice Xa21 disease resistance gene family. Plant Cell. 1997 9(8):1279-87. PUBMED.
Maize poly-UbiA genes
The most parsimonious duplication tree (DTEXPLORE) is identical to the most parsimonious phylogeny (DNAPENNY) and requires 87 parsimony steps. DTSCORE finds the same duplication tree. There is only one potential root for this duplication tree, situated "above" the 2-duplication.
Human T cell receptor gamma variable genes
The most parsimonious duplication tree (DTEXPLORE) is identical to the most parsimonious phylogeny (DNAPENNY). We showed in our MBE paper that this identity is very robust, and cannot be due to chance (the probability of this identity to happen by chance is 0.038). Once again, DTSCORE finds the same duplication tree. There are four potential roots for this duplication. We showed that the root is likely to be located on the branch leading to V8. Associated article : Elemento et al. Reconstructing the duplication history of tandemly repeated genes. Mol Bio Evol. 2002 19:278-288. PUBMED.
Human Immunoglobulin lamda constant genes
The most parsimonious duplication tree (DTEXPLORE) is identical to the most parsimonious phylogeny (DNAPENNY). DTSCORE finds the same duplication tree. There are 2 potential roots for this duplication tree. We did not accurately determine which one of these two is the best one. Associated article : Elemento et al. Reconstructing the duplication history of tandemly repeated genes. Mol Bio Evol. 2002 19:278-288. PUBMED.
KpnI repetitive sequence
From the Genbank flat file for a human herpesvirus-6 region (accession number D11134), this sequence contains 28 copies of a tandemly repeated 104-107 bp element, each of which (with one exception) contains a recognition site for KpnI. Using the Tandem Repeat Finder tool, I actually found 29.4 repeats (29 repeats and the 5' 40% of a 30th one). The raw sequences are available here. On this dataset DNAPARS finds 138 equally parsimonious trees, each requiring 52 parsimony steps. There are two many sequences for DTEXPLORE, so we used DTSCORE to obtain a tree. The tree found by DTSCORE requires 61 parsimony steps, which is much higher than the parsimony trees. Then we generated 100 pseudosamples, ran DTSCORE again each of these pseudosamples, and created the consensus tree (CONSENSE). The consensus tree (shown here) is almost 100% identical to the initial tree and also requires 61 parsimony steps.
GBP-130 duplicated domains
The amino acid sequence of the Plasmodium falciparum GBP-130, deduced from the cloned and sequenced gene, reveals that the protein contains 11 highly conserved 50 amino acid repeats. The 11 repeats were extracted from the Genbank record M12897. DNAPENNY finds 6 equally parsimonious trees, with 30 steps, and none of them is a duplication tree. The DTSCORE duplication tree necessitates 33 steps. This tree is shown here.