Prank is not given a guide tree inside sate

[smirarab]

Prank is called as follows

invoc = [self.exe, '-once', '-noxml', '-notree', '-nopost', '+F', '-quiet', '-matinitsize=5', '-uselogs', '-d=%s' % seqfn, '-o=%s' % alignedfn]

Issues with this:

1. No guide tree is give.
2. -once makes it run only one iteration instead of two. When there is no guide tree given, Prank strongly suggests doing two iterations (default).

We should ideally prune the current (or best) tree and give it to prank. If not, we should at least do the default two iteration Prank (which is slow!)