== 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)
* `-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 ====
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.
-=== Example ===
+==== 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 ===
`rio gene_trees.nh species.xml outtable.tsv log.txt`
+
`rio gene_trees.nh species.xml outtable.tsv log.txt -r=outgroup -o=XVL1_ECOLI`
+`rio gene_trees.nh species.xml outtable.tsv log.txt -f=0 -l=49`
+
=== Example files ===
* [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]
* [http://forester.googlecode.com/files/species_tree_rio.xml species tree file]