== Usage ==
-{{{
-java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]
-}}}
+
+`java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]`
=== Options ===
* `-f=<first>` : first gene tree to analyze (0-based index) (default: analyze all gene trees)
The species tree is allowed to have nodes with more than two descendants (polytomies), as long as the (slower) GSDIR ([GSDI GSDI] re-rooting) algorithm is used.
-==== Note ====
-Since the Java memory default allocation too small for even moderately large data-sets, it is necessary to increase it with the `-Xmx2048m` command line option.
+==== Note about memory ====
+Since the Java memory default allocation is too small for even moderately large data-sets, it is necessary to increase it with the `-Xmx2048m` command line option.
=== Examples ===