== 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)
- * `-l=<last>` : last gene tree to analyze (0-based index)
+ * `-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 gene trees ideally are in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format, with taxonomy and sequence data in appropriate fields; but can also be in New Hamphshire (Newick) or Nexus format, as long as species information can be extracted from the gene names (e.g. "HUMAN" from "BCL2_HUMAN") ([http://forester.googlecode.com/files/gene_trees_rio.nh example]).
+The gene trees ideally are in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format, with taxonomy and sequence data in appropriate fields; but can also be in New Hamphshire (Newick) or Nexus format, as long as species information can be extracted from the gene names (e.g. "HUMAN" from "BCL2_HUMAN") ([https://forester.googlecode.com/svn/forester/examples/rio/gene_trees_rio.nh example]).
All gene trees must be *completely binary*.
==== Species tree ====
-The species tree ideally is in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format, but can also be in New Hamphshire (Newick) or Nexus format ([http://forester.googlecode.com/files/species_tree_rio.xml example]).
+The species tree ideally is in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format, but can also be in New Hamphshire (Newick) or Nexus format ([https://forester.googlecode.com/svn/forester/examples/rio/species_tree_rio.xml example]).
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]
+ * [https://forester.googlecode.com/svn/forester/examples/rio/gene_trees_rio.nh gene trees file]
+ * [https://forester.googlecode.com/svn/forester/examples/rio/species_tree_rio.xml species tree file]
== References ==