fixing the alignment test
added recursion limit, removed debug line
updating upp to create backbone, mafft section complete
added backbone creation
fixing setup to support new upp
fixing backbone
added auto backbone/alignment selection.
fixed parameters
fixed protein to amino
minor change added type for sate
still fixing sate bug
updated instructions for installation
added readme
modified readme, preparing to merge
prepping to merge
Merge branch 'sepp2'

Conflicts: