Mgenome is designed to find the optimal trees for multiple genome rearrangement by signed reversals. The problem is modeled as: For a given collection of genomes represented by signed permutations on genes, find a tree to connect the given genomes by reversal paths such that the number of all signed reversals is minimized.
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S. Wu and X. Gu,
Algorithms for multiple genome rearrangement by signed reversals,
Pacific Symposium on Biocomputing, 8(2003), 363-374.