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 -Xmx1024m -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
-
- * -q : name for query (sequence/node)
+== Usage ==
- * -s : sort (default: 2)
+`java -Xmx2048m -cp forester.jar org.forester.application.rio [options] <gene trees> <species tree> <outfile> [logfile]`
- * -u : to output ultra-paralogs (species specific expansions/paralogs)
+=== 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)
- * -cu: cutoff for ultra-paralog output (default: 50)
+
+==== 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") ([https://forester.googlecode.com/svn/forester/examples/rio/gene_trees_rio.nh example]).
+All gene trees must be *completely binary*.
-==== Sort ====
- * 0: orthologies
- * 1: orthologies > super orthologies
- * 2: super orthologies > orthologies
+==== 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 ([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.
-==== 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").
-==== Species tree ====
-Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species.xml 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 outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60`
+`rio gene_trees.nh species.xml outtable.tsv log.txt`
-`rio gene_trees.nh species.xml -t=outtable`
+`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`
-<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>
+ * [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 ==