X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=8bafb64c0a51ea3fe2cdbc47689d65d8ad857f19;hb=bb367671ad9b009584da301ad4591c2f1e8f0901;hp=144d2f136e6f4f2cb011fda20d46c21ec5ae5dd9;hpb=12dcbed140836c15a8294e2b575f72d86909bbd5;p=jalview.git diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 144d2f1..8bafb64 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -6,54 +6,35 @@ 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 -Xmx2048m -cp forester.jar org.forester.application.rio [options] [outfile] +java -Xmx2048m -cp forester.jar org.forester.application.rio [options] [logfile] }}} -=== Options === - - * -co: cutoff for ortholog output (default: 50) - - * -t : file-name for output table of all vs. all ortholgy support - - * -q : name for query (sequence/node), if this is used, `[`outfile`]` is required as well - - * -s : sort (default: 2) - - * -u : to output ultra-paralogs (species specific expansions/paralogs) - - * -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 and a `[`outfile`]` are required. - -==== Sort ==== +=== Options === - * 0: orthologies - * 1: orthologies > super orthologies - * 2: super orthologies > orthologies + * -b : to use SDIR instead of GSDIR (faster, but non-binary species trees are disallowed) + ==== 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]). - -==== Species tree ==== -Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species_tree_rio.xml example]). +All gene trees must be *completely binary*. -=== Examples === -`rio gene_trees_rio.nh species_tree_rio.xml outfile -q=D_HUMAN -t=outtable -u -cu=10 -co=10` +==== Species tree ==== +Must be in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format ([http://forester.googlecode.com/files/species_tree_rio.xml example]). +The species tree is allowed to have nodes with more than two descendents (polytomies), as long as the (slower) GSDIR ([GSDI GSDI] re-rooting) algorithm is used. -`rio gene_trees.nh species.xml outfile -q=BCL2_HUMAN -t=outtable -u -cu=60 -co=60` -`rio gene_trees.nh species.xml -t=outtable` +=== Example === +`rio gene_trees.nh species.xml outtable.tsv log.txt` === 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] - * [http://forester.googlecode.com/files/rio_outfile.txt output] (for query "D_HUMAN") - + == References ==