inprogress

[jalview.git] / wiki / RIO.wiki

diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki
index a10b4eb..6209ad7 100644 (file)
--- a/wiki/RIO.wiki
+++ b/wiki/RIO.wiki
@@ -8,35 +8,41 @@ RIO (Resampled Inference of Orthologs) is a method for automated phylogenomics b
 
 
 == 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)
-  * -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) 
+  * `-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]).
+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 ==