JAL-2797 standalone and embedded implementations of AptxFrame

[jalview.git] / wiki / genetreepreprocessing.wiki

diff --git a/wiki/genetreepreprocessing.wiki b/wiki/genetreepreprocessing.wiki
index 0c977cc..25348f9 100644 (file)
--- a/wiki/genetreepreprocessing.wiki
+++ b/wiki/genetreepreprocessing.wiki
@@ -1,13 +1,27 @@
-#Gene tree preprocessing
+#summary preprocessing of gene trees for speciation/duplication inference
 
-= Introduction =
+= Gene tree preprocessing =
 
-Add your content here.
+== Purpose ==
 
+Use EBI database to add species information to a gene tree which has sequence identifiers as labels.
 
-= Details =
+== Usage == 
+{{{
+java -Xmx1024m -cp
+path/to/forester.jar org.forester.application.gene_tree_preprocess <input tree in NH, NHX, Nexus, or phyloXML>
+}}}
 
-Add your content here.  Format your content with:
-  * Text in *bold* or _italic_
-  * Headings, paragraphs, and lists
-  * Automatic links to other wiki pages
\ No newline at end of file
+
+
+== Details ==
+
+Output consists of three files:
+  * input-name_preprocessed_gene_tree.phylo.xml
+  * input-name_species_present.txt
+  * input-name_removed_nodes.txt
+
+
+== Download ==
+
+Download forester.jar here: http://code.google.com/p/forester/downloads/list
\ No newline at end of file