X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FRIO.wiki;h=6209ad70348f68bc825d991678948d7f624c5069;hb=9a7395cfe0de3a3405ac9e6105d0577bc45d30ff;hp=68e5a3e7d7318bf1cc2bba7e02d0b3d1e74d2e82;hpb=690c48ebd0822147b078018c63b640c1ee265d5d;p=jalview.git

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.