Actually removed dependence on Bio.Seq.

Before I didn’t change helix.py and junction.py. Those libraries didn’t
actually call Bio.Seq, but they tried to import it.
intermediate work on changing the threading procedure
changed workflow in threading

Changed ‘threadTogether’ function so that it is called iteratively,
progressively adding sequences to a central region, rather than taking
each sequence and ordering it in a particular order. This is moving
towards being able to have multiple junctions.
Merge branch 'changeThreading'