X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=21de730628be95765d9f6c186b8a34fa20aa707d;hb=c3f7a7af2eeb49f8847b5b955c8960097257228e;hp=6d69e3caa0abfccbf809a5d068ff864766c70c18;hpb=5665c369cb106aa78c8f9605116cdd4bec3a792e;p=jalview.git

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index 6d69e3c..21de730 100644
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -6,54 +6,44 @@
 
 RIO (Resampled Inference of Orthologs) is a method for automated phylogenomics based on explicit phylogenetic inference. RIO analyses are performed over resampled phylogenetic trees to estimate the reliability of orthology assignments.
 
-== Usage == 
-{{{
-java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees file> <species tree file> [outfile]
-}}}
-=== Options ===
-
-  * -co: cutoff for ortholog output (default: 50) 
-  
-  * -t : file-name for output table of all vs. all ortholgy support
-  
-  * -q : name for query (sequence/node), if this is used, `[`outfile`]` is required as well
-
-  * -s : sort (default: 2)
-
-  * -u : to output ultra-paralogs (species specific expansions/paralogs)
-
-  * -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.
+== Usage == 
 
-==== Sort ====
+`java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]`
 
-  * 0: orthologies
-  * 1: orthologies > super orthologies
-  * 2: super orthologies > orthologies
+=== 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, 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]).
+All gene trees must be *completely binary*.
+
 
 ==== Species tree ====
-Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] 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  ([http://forester.googlecode.com/files/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. 
 
 
-=== Examples ===
-`rio gene_trees_rio.nh species_tree_rio.xml outfile -q=D_HUMAN -t=outtable -u -cu=10 -co=10`
+==== 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.
 
-`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`
+=== 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]
-  * [http://forester.googlecode.com/files/rio_outfile.txt output] (for query "D_HUMAN")
-
+  
 
 == References ==