Remove deprecated functions, add new

Remove comparetwo, add parse.clades and load.trees
New compare.n with clade translation table

rwty.comparen object now returns a clade table that uses factor numbers
instead of tip number lists, also returns a clade table that translates
factors to number lists and tip label lists.
First draft of load.trees.R

New function that does the following

Take a tree file name, load file into memory
Unroot trees and reset to class multiPhylo (lapply deletes class info)
Check for a .p file for the chain and load it if it exists
Return an object containing the trees and p table, if it exists.