ENH|DEP: adding public function for creating identity substitution matrices. this is immediately getting a deprecation warning however, as we will soon be adding a SubstitutionMatrix class that will include this functionality but we need the functionality in the meantime for a few special cases
ENH: modified to support DNA or RNA by default
TST: fixed tests failing due to previous commit
DOC: removed see also, as this isn't really specific to nucleotide alignment
Merge pull request #592 from gregcaporaso/issue-535

adding public function for creating identity substitution matrices