* -co: cutoff for ortholog output (default: 50)
- * -t : file-name for output table
+ * -t : file-name for output table of all vs. all ortholgy support
- * -q : name for query (sequence/node), if this is bing used, '*'[outfile'*'] is required as well
+ * -q : name for query (sequence/node), if this is used, `[`outfile`]` is required as well
* -s : sort (default: 2)
* -cu: cutoff for ultra-paralog output (default: 50)
+==== Note ====
+
+Either output of all vs. all ortholgy support with -t=`<`output table`>` and/or output for one query sequence with -q=`<`query name`>` and a `[`outfile`]` are required.
+
==== Sort ====
* 0: orthologies
* 2: super orthologies > orthologies
==== 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").
+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]).
==== Species tree ====
-Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species.xml example]).
+Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species_tree_rio.xml example]).
=== Examples ===
+`rio gene_trees_rio.nh species_tree_rio.xml outfile -q=D_HUMAN -t=outtable -u -cu=10 -co=10`
+
`rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60`
`rio gene_trees.nh species.xml -t=outtable`
-<wiki:comment>
=== Example files ===
- * [http://forester.googlecode.com/files/wnt_gene_tree.xml gene tree]
- * [http://forester.googlecode.com/files/species.xml species tree]
- * [http://forester.googlecode.com/files/wnt_gsdi_log.txt log file (output)]
-</wiki:comment>
+ * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]
+ * [http://forester.googlecode.com/files/species_tree_rio.xml species tree file]
+ * [http://forester.googlecode.com/files/rio_outfile.txt output] (for query "D_HUMAN")
+
== References ==