-some general code cleanup
-added the big tree plausibility checking option -f R.
 This option allows to assess the plausibility of a very large tree that can not
 be inspected visually any more by computing its RF distance to many smaller (better quality) trees
 that contain a subset of taxa of the large tree.
 To invoke: ./raxmlHPC-SSE -f R -m GTRCAT -t largeTree -z smallReferenceTrees -n T1
 where file "largeTree" contains the huge tree and "smallReferenceTrees" the smaller
 reference trees against which we want to check.