The cleaning for Bio::SimpleAlign is 99% finished, though a few tests may be needed. Here are the major improvements on Bio::SimpleAlign
1. MSA modifying and selection methods are more consistent and easier to use. I have enabled multiple/reverse selections for all sequences/columns selection methods, and change the names to be more understandable.
2. gap chars/missing chars are more consistent in the package
3. Some redundant methods are removed. The methods are moved to more reasonable categories.
4. Some methods are renamed. Methods selecting/giving objects are capitalized, e.g. each_seq to each_Seq. (Though each_Seq and add_Seq may cause inconsistency in some packages related with Bio::SimpleAlign, because they are so widely used. I will find them and replace them).