Updated startInM/X/Y to reflect probabilities based on numbers of residues and box-width, instead of fixed probabilities.  Doesn't pass symmetric TotalProbability test, but otherwise seems to work fine.
Updated startInM/X/Y to reflect probabilities based on numbers of residues and box-width, instead of fixed probabilities.  Doesn't pass symmetric TotalProbability test, but otherwise seems to work fine.

davidsoergel/phyloutils