}}}
=== Options ===
- * -f=<first> : first gene tree to analyze (0-based index)
- * -l=<last> : last gene tree to analyze (0-based index)
+ * `-f=<first>` : first gene tree to analyze (0-based index)
+ * `-l=<last>` : last gene tree to analyze (0-based index)
* -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)