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[jalview.git] / wiki / genetreepreprocessing.wiki

diff --git a/wiki/genetreepreprocessing.wiki b/wiki/genetreepreprocessing.wiki
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--- a/wiki/genetreepreprocessing.wiki
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-= Gene tree Preprocessing =
+#summary preprocessing of gene trees for speciation/duplication inference
 
-Usage: 
-java -Xms32m -Xmx1024m -cp
+= Gene tree preprocessing =
+
+== Purpose ==
+
+Use EBI database to add species information to a gene tree which has sequence identifiers as labels.
+
+== Usage == 
+{{{
+java -Xmx1024m -cp
 path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
+}}}
 
 
 
+== Details ==
 
+Output consists of three files:
+  * input-name_preprocessed_gene_tree.phylo.xml
+  * input-name_species_present.txt
+  * input-name_removed_nodes.txt
 
 
-= Details =
+== Download ==
 
-Add your content here.  Format your content with:
-  * Text in *bold* or _italic_
-  * Headings, paragraphs, and lists
-  * Automatic links to other wiki pages
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+Download forester.jar here: http://code.google.com/p/forester/downloads/list
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