From: cmzmasek@gmail.com Date: Wed, 28 Nov 2012 23:13:26 +0000 (+0000) Subject: Edited wiki page RIO through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=659fcb38ab12b005a287c643f6946d83f5bb97ab;p=jalview.git Edited wiki page RIO through web user interface. --- diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 180a553..1cc4ada 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -32,37 +32,23 @@ path/to/forester.jar org.forester.application.rio [options] 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 phyloXML,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 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` +`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 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 == @@ -71,7 +57,6 @@ Zmasek CM and Eddy SR "RIO: Analyzing proteomes by automated phylogenomics using 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