Note: Also need ILP solver Gurobi (information on free academic licenses here).
Copy gurobi.jar (found in a subdirectory called lib somewhere in the gurobi directory) to the same directory as LP.jar.
Usage: Usage: java -jar LP.jar [-s] input where input is a file (or "stdin") containing a pair of rooted binomial trees in Newick format with no names for the internal nodes
(see, e.g., https://en.wikipedia.org/wiki/Newick_format for more information on this format)
The optional -s forces the program to use the names of the leaves instead of the number of the node. (Otherwise, the numbering of the nodes is according to the order they appear in the first tree of the input.)
Usage: java -jar MAF2approx.jar [-s] input (similar usage to LP.jar above)
Can be downloaded from Chris Whidden's github page for rspr. Example inputs here.