Revert to use one-sided SH test
Fix white space
Fix check for rooted, binary tree.  Fix more white space.
Update libraries (not dependent on PLY).  Remove treefix_raxml packaging files.
Fix bugs and add short option for specifying seed

- Specify seed with "-x" in addition to "--seed"
- Update library (error fix in treelib)
- Add missing import to rangerdtlmodel