== 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 file> <species tree file> [outfile]
}}}
=== Options ===
* -co: cutoff for ortholog output (default: 50)
- * -t : file-name for output table
+ * -t : file-name for output table of all vs. all ortholgy support
- * -q : name for query (sequence/node)
+ * -q : name for query (sequence/node), if this is used, `[`outfile`]` is required as well
* -s : sort (default: 2)
* -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.
+
==== Sort ====
* 0: 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]).
==== 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"`.
+Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species_tree_rio.xml example]).
-=== 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")
+=== 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`
-
-=== Example ===
-`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml`
+`rio gene_trees.nh species.xml -t=outtable`
=== 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]
+ * [http://forester.googlecode.com/files/rio_outfile.txt output] (for query "D_HUMAN")
== 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