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diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index a875f25..ac4db98 100644
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -1,25 +1,62 @@
-#summary preprocessing of gene trees for speciation/duplication inference
+#summary generalized speciation duplication inference
-= Generalized Speciation Duplication Inference
+= Generalized Speciation Duplication Inference =
== Purpose ==
-Infer duplication events on a gene tree given a trusted species tree.
+To infer duplication events on a gene tree given a trusted species tree.
== Usage ==
{{{
java -Xmx1024m -cp
-path/to/forester.jar org.forester.application.gene_tree_preprocess
+path/to/forester.jar org.forester.application.gsdi [-options]
}}}
+=== Options ===
+ * -g: to allow stripping of gene tree nodes without a matching species in the species tree
+
+ * -m: use most parimonious duplication model for GSDI: assign nodes as speciations which would otherwise be assiged as potential duplications due tp polytomies in the species tree
+ * -q: to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)
-== Details ==
+ * -b: to use SDIse algorithm instead of GSDI algorithm (for binary species trees)
-Output consists of three files:
- * input-name_preprocessed_gene_tree.phylo.xml
- * input-name_species_present.txt
- * input-name_removed_nodes.txt
+==== Gene tree ====
+Must be in phyloXM format, with taxonomy and sequence data in appropriate fields ([http://forester.googlecode.com/files/wnt_gene_tree.xml example]).
+
+==== Species tree ====
+Must be in phyloXML format unless option -q is used ([http://forester.googlecode.com/files/species.xml example]).
+
+=== Output ===
+
+Besides the main output of a gene tree with duplications and speciations assigned to all of its internal nodes, this program also produces the following:
+ * a log file, ending in `"_gsdi_log.txt"` ([http://forester.googlecode.com/files/wnt_gsdi_log.txt example])
+ * a species tree file which only contains external nodes with were needed for the reconciliation, ending in `"_species_tree_used.xml"`
+ * if the gene tree contains species with scientific species names such as "Pyrococcus horikoshii strain ATCC 700860" and if a mapping cannot be establish based on these, GSDI will attempt to map by removing the "strain" (or "subspecies") information, these will be listed in a file ending in `"_gsdi_remapped.txt"`.
+
+=== Taxonomic mapping between gene and species tree ===
+
+GSDI can establish a taxonomic mapping between gene and species tree on the following three data fields:
+ * scientific names (e.g. "Pyrococcus horikoshii")
+ * taxonomic identifiers (e.g. "35932" from uniprot or ncbi)
+ * taxonomy codes (e.g. "PYRHO")
+
+
+
+=== Example ===
+`gsdi -g -q gene_tree.xml tree_of_life.nwk out.xml`
+
+
+=== Example files ===
+ * [http://forester.googlecode.com/files/wnt_gene_tree.xml gene tree]
+ * [http://forester.googlecode.com/files/species.xml species tree]
+ * [http://forester.googlecode.com/files/wnt_gsdi_log.txt log file (output)]
+
+
+== Reference ==
+
+Zmasek CM and Eddy SR "A simple algorithm to infer gene duplication and speciation events on a gene tree" [http://bioinformatics.oxfordjournals.org/content/17/9/821.abstract Bioinformatics, 17, 821-828]
+
== Download ==