MatrixGen 0.46 Released

Well, 0.46 is released. It contains loads of new useful features (The code went through a little beautification as well). Most notably are the following:

-New command line interface. This interface was necessary to really get a convergant matrix very easily.

-Loads of new options available from the command line interface (output matrix precision, assume transitions, scaling factors, and more).

-Support for DNA as well as AMINO ACID alignments.

-Treating ambiguous symbols as any of the symbols they could be, instead of treating them as unique symbols.