work on data buffer for aLeaves MAFFT suite + clean up

[jalview.git] / wiki / RIO.wiki

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index 3d1f40b..6d69e3c 100644 (file)
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -26,8 +26,7 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene tre
 
 ==== Note ====
 
-Either output of all vs. all ortholgy support with -t and/or output for 
-one query sequence with -q and a  `[`outfile`]` are required.
+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 ====
 
@@ -36,24 +35,25 @@ one query sequence with -q and a  `[`outfile`]` are required.
   * 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 ==