Mashtree plugins are executed such that a mashtree database is the first positional parameter. Flag options are allowed. Additional tables within the database might get created, but overwriting the DISTANCE table is not allowed.
For more information on the standard database, please see the documentation.
This plugin optimizes distances between all genomes. Currently only uses Dijkstra's algorithm but potentially could be expanded.
Usage: mashtree_optimize.pl [options] mashtree.sqlite