* `-l=<last>` : last gene tree to analyze (0-based index) (default: analyze all gene trees)
* `-r=<re-rooting>` : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications)
* `-o=<outgroup>` : for rooting by outgroup, name of outgroup (external gene tree node)
- * `-b` : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed)
+ * `-b` : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed, as are all options)
==== Gene trees ====