Input: a gene tree and a signed order representing the gene's arrangement on the chromosome for a TAG cluster in a single species.
Output: a parsimonious sequence of tandem duplication(s), inverted duplication(s), inversion(s) and deletion(s) explaining the input.
The gene tree must be in Newick format. It can contain branch length and bootstrap values, but these are not considered by the present version of the algorithm. If the gene tree is unrooted, the algorithm will be applied once for each possible root position, and results will be shown for the position leading to the lowest cost histories. The maximum size is 30 leaves for the gene tree. You can give up to 10 alternative gene trees for the same cluster as input, and the algorithm will be applied for each one of them.
The gene order is a sequence a genes separated by spaces in parentheses. The genes must have the same labels as in the gene trees, at the exception of the minus signs ("-") used to indicate genes on the opposite DNA strand.
The cost of an event is a+(b * size), where "size" corresponds to the number of genes involved in the event.
Please read the paper to see the capabilities and limitations of the algorithm.