Allows the user to define distances between different bases. E.g. An A-T should get a smaller difference as an A-G, so the corresponding matrix elements should be set to 1.0 and 2.0.
NOTES
Before the algorithm starts, all matrix values will be multiplied by a factor, so that the average matrix value (except the diagonal) gets a value of one !!!
To save a user matrix use <Properties/Save Properties> menu item.