From: cmzmasek@gmail.com Date: Fri, 24 Jan 2014 02:28:16 +0000 (+0000) Subject: Edited wiki page RIO through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ffb7cee53afea2fe51e3469c54c7f343b7a509ae;p=jalview.git Edited wiki page RIO through web user interface. --- diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 68e5a3e..6209ad7 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -20,12 +20,12 @@ RIO (Resampled Inference of Orthologs) is a method for automated phylogenomics b ==== 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]). +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") ([https://forester.googlecode.com/svn/forester/examples/rio/gene_trees_rio.nh example]). All gene trees must be *completely binary*. ==== 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 ideally is in [http://www.biomedcentral.com/1471-2105/10/356/ phyloXML] format, but can also be in New Hamphshire (Newick) or Nexus format ([https://forester.googlecode.com/svn/forester/examples/rio/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.