BUG: Change Sequence to BiologicalSequence

Making this change required that the output of any BiologicalSequence
object be casted to a string to ensure backwards compatibility
API: Update use of the skbio API
API: SequenceCollection does not provide NamedSeqs

This is a property that the previous SequenceCollection objects did
provide (in cogent).
TST API: Fix broken test because of deprecated API

This test relied on counting the number of sequences in the alignment
object, the new API provides a sequence_count method that makes this
more straight forward.
API: Update use of Sequence API

The parsed fasta records in SequenceCollection split the identifiers on
blankspaces to retrieve the description of each sequences, this is
required the code to be updated because it was previously checking for
an identifer plus description combo.
TST: clean up tests for MinimalRfamParser