X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=21de730628be95765d9f6c186b8a34fa20aa707d;hb=80160ba33817d2f7f35171ec5f430b23467fff2d;hp=180a553227c443cd9afb98f8a4a7fdb5fcfa3cca;hpb=2193ea2c5f1e9b6bc98fd07c96007203c4be4a91;p=jalview.git diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 180a553..21de730 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -6,71 +6,53 @@ 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) +== Usage == -==== Sort ==== +`java -Xmx2048m -cp forester.jar org.forester.application.rio [options] [logfile]` - * 0: orthologies - * 1: orthologies > super orthologies - * 2: super orthologies > orthologies +=== Options === + * `-f=` : first gene tree to analyze (0-based index) (default: analyze all gene trees) + * `-l=` : last gene tree to analyze (0-based index) (default: analyze all gene trees) + * `-r=` : re-rooting method for gene trees, possible values or 'none', 'midpoint', or 'outgroup' (default: by minizming duplications) + * `-o=` : 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, as are all options) + ==== 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]). +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*. -=== 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"`. +==== 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. -=== 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") +==== Note about memory ==== +Since the Java memory default allocation is too small for even moderately large data-sets, it is necessary to increase it with the `-Xmx2048m` command line option. +=== Examples === +`rio gene_trees.nh species.xml outtable.tsv log.txt` -=== Example === -`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml` +`rio gene_trees.nh species.xml outtable.tsv log.txt -r=outgroup -o=XVL1_ECOLI` +`rio gene_trees.nh species.xml outtable.tsv log.txt -f=0 -l=49` === 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 ==