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
-path/to/forester.jar org.forester.application.rio [options] <gene trees file> <species tree file> [outfile]
+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) (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)
- * -co: cutoff for ortholog output (default: 50)
-
- * -t : file-name for output table
- * -q : name for query (sequence/node)
-
- * -s : sort (default: 2)
-
- * -u : to output ultra-paralogs (species specific expansions/paralogs)
-
- * -cu: cutoff for ultra-paralog output (default: 50)
-
-==== Sort ====
-
- * 0: orthologies
- * 1: orthologies > super orthologies
- * 2: super orthologies > orthologies
-
==== Gene trees ====
-The gene trees ideally are in phyloXML, 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]).
+All gene trees must be *completely binary*.
-==== Species tree ====
-Must be in phyloXML format ([http://forester.googlecode.com/files/species.xml example]).
-
-=== Output ===
-
-Besides the main output of a gene tree with duplications and speciations assigned to all of its internal nodes, this program also produces the following:
- * a log file, ending in `"_gsdi_log.txt"` ([http://forester.googlecode.com/files/wnt_gsdi_log.txt example])
- * a species tree file which only contains external nodes with were needed for the reconciliation, ending in `"_species_tree_used.xml"`
- * if the gene tree contains species with scientific species names such as "Pyrococcus horikoshii strain ATCC 700860" and if a mapping cannot be establish based on these, GSDI will attempt to map by removing the "strain" (or "subspecies") information, these will be listed in a file ending in `"_gsdi_remapped.txt"`.
-
-=== Taxonomic mapping between gene and species tree ===
-
-GSDI can establish a taxonomic mapping between gene and species tree on the following three data fields:
- * scientific names (e.g. "Pyrococcus horikoshii")
- * taxonomic identifiers (e.g. "35932" from uniprot or ncbi)
- * taxonomy codes (e.g. "PYRHO")
+==== 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 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 ===
-`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml`
+`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`
=== 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)]
-
+ * [http://forester.googlecode.com/files/gene_trees_rio.nh gene trees file]
+ * [http://forester.googlecode.com/files/species_tree_rio.xml species tree file]
+
== References ==
Zmasek CM and Eddy SR "RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs" [http://www.biomedcentral.com/1471-2105/3/14/ BMC Bioinformatics 2002, 3:14]
Zmasek CM and Eddy SR "A simple algorithm to infer gene duplication and speciation events on a gene tree" [http://bioinformatics.oxfordjournals.org/content/17/9/821.abstract Bioinformatics, 17, 821-828]
-
+Han M and Zmasek CM "phyloXML: XML for evolutionary biology and comparative genomics" [http://www.biomedcentral.com/1471-2105/10/356/ BMC Bioinformatics 2009, 10:356]
+
== Download ==
git://source.jalview.org / jalview.git / blobdiff