-added even more verbose PHYLIP-like formatted output for supported and conflicting bipartitions
 for the IC and TC score calculation from Rokas and Salichos 2013. Note that, the verbose output
 for all IC and TC-related calculations is activated by -C
-fixed a bug in the model parameter optimization routine
-added an option -X that will execute a randomized addition order parsimony tree
 building algorithm and then exit (as opposed to -y) without doing any parsimony-based SPRs.
 This is helful for generating more diverse (topologically different) parsimony-based starting tree
 on whole-genome alignemnts that often show a very clear signal for one or just a few parsimony trees.