From 2193ea2c5f1e9b6bc98fd07c96007203c4be4a91 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 28 Nov 2012 23:09:17 +0000 Subject: [PATCH] Created wiki page through web user interface. --- wiki/RIO.wiki | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 wiki/RIO.wiki diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki new file mode 100644 index 0000000..180a553 --- /dev/null +++ b/wiki/RIO.wiki @@ -0,0 +1,77 @@ +#summary resampled inference of orthologs + += RIO: Resampled Inference of Orthologs = + +== Purpose == + +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] [outfile] +}}} +=== Options === + + * -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"). + +==== 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") + + + +=== Example === +`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml` + + +=== 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)] + + +== 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] + + + +== Download == + +Download forester.jar here: http://code.google.com/p/forester/downloads/list \ No newline at end of file -- 1.7.10.2