Bio::SimpleAlign - follow some perl best practices

* use warnings
* use parent instead of base
* declare variable with "our" instead of use vars
* remove unecessary BEGIN block
Bio::Align::Utilities - new function most_common_sequences

* adds a new subroutine that takes a Bio::AlignI object and finds the sequence
that appears repeated most often.
Bio::Align::Utilities - follow some perl best practices.

* use warnings;
* declare variables with "our" instead of "use vars"
* don't set Exporter at runtime and make things simpler
* drop unecessary BEGIN block
Fix nonsense in code comments.