clean junk code from plawty.r
remove check for unrooted trees rom tree.dist.matrix.liam

because it didn't seem to work on multiphylo lists. For reasons I
didn't figure out yet, a list of unrooted trees returns a list of
TRUE's when you do this:

sapply(unclass(trees),is.rooted))

This is not the intended behaviour. And in any case, we should move all
of this to a function that reads in trees and does these checks once
only.
add shell for tree loading

Things that should go in here, perhaps:

1. Check that all trees are unrooted, and unroot if necessary
2. Calculate prop.part on all trees in the list
3. Option to read in a .p file
4. file format options, e.g. tree.format="Nexus", p.format = "csv"…

We could then return an object with the tree list and the prop.part
list. That could feed into most other functions in RWTY, and would save
time.