removed functionality for synonymous/nonsynonymous calculations
Added get functions for  (sub width) and the number of valid positions remaining following thresholding (sub valid_positions).
added _alphabet_check() for handling unexpected
characters
added check for whether there are any valid positions
added initial code for accepting a binary mask in initialize() which specifies which positions to analyze (default = analyze all positions)
bug fixes for recently added functionality
added function to print probabilities by position
altered unexpected symbols handling and added rna option
cleanup
Modifications to allow dna, rna, or protein analysis. Generalized the matrices construction with _build_matrix(). Added functionality to handle alternate gap symbols.
made alterations to prevent counting comparisons of a position to itself in the coverage calculations used for both epd and apd
added new apd functions (fast_apd and converntional_apd) and altered functions to facilitate the usage of the four methods. Incorporated changes from the exact branch including a new _end character.
added Fernando's alterations to the epd and variance calculations
merge from dev