From: cmzmasek@gmail.com Date: Thu, 20 Dec 2012 01:14:57 +0000 (+0000) Subject: Edited wiki page RIO through web user interface. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1a8cad845aa24435505aff7998bf9a90697202ac;p=jalview.git Edited wiki page RIO through web user interface. --- diff --git a/wiki/RIO.wiki b/wiki/RIO.wiki index 8bafb64..79c40b7 100644 --- a/wiki/RIO.wiki +++ b/wiki/RIO.wiki @@ -13,7 +13,10 @@ java -Xmx2048m -cp forester.jar org.forester.application.rio [options] : first gene tree to analyze (0-based index) + * -l= : last gene tree to analyze (0-based index) + * -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) @@ -23,8 +26,8 @@ All gene trees must be *completely binary*. ==== 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. +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. === Example ===