DupLoCut - Duplication Loss Evolution by Branch and Cut ======================================================= This software computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model. DEPENDENCIES ============ You have to install the following libraries to compile DupLoCut: - lemon (http://lemon.cs.elte.hu) - seqan (www.seqan.de) - cplex (www.ibm.com/software/integration/optimization/cplex-optimizer) INSTALLATION ============ $ cmake . $ make DupLoCut Running DupLoCut ================ $ DupLoCut -i -g -o Program parameters: tree-file phylogenetic tree in Newick format without branch lengths genome-file textfile containing the gene sequences. output-prefix files .tree and .median will be generated For more options, call $ DupLoCut --help