Parsimony¶

Notes on solving the Large Parsimony problem with nearest neighbor interchange. Here are two simple test examples. The first shows a tree with four leaf nodes and two internal nodes. The minimal parsimony solution consists of swapping two leaf nodes to reduce the overall hamming distance.

Very simple test example - solution is to swap one C with one G, resulting in a tree with a minimum parsimony hamming distance of 1.

Another test example - this time the solution is to swap two internal nodes, as shown below.