Update skbio.sequence to use BiologicalSequence.copy

k_words() now returns BiologicalSequence objects. Removed unused constructor parameters.
Update skbio.alignment to use BiologicalSequence.copy/__getitem__

Deprecated Alignment.majority_consensus constructor parameter.  BiologicalSequence.__getitem__ now supports list of indices to keep. Removed broken constructor argument to Alignment.k_word_frequencies.