inprogress

[jalview.git] / wiki / GSDI.wiki

diff --git a/wiki/GSDI.wiki b/wiki/GSDI.wiki
index 928dbce..ac4db98 100644 (file)
--- a/wiki/GSDI.wiki
+++ b/wiki/GSDI.wiki
@@ -22,10 +22,17 @@ path/to/forester.jar org.forester.application.gsdi [-options] <gene tree in phyl
   * -b: to use SDIse algorithm instead of GSDI algorithm (for binary species trees)
 
 ==== Gene tree ====
-Must be in phyloXM format, with taxonomy and sequence data in appropriate fields.
+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.
+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 ===
 
@@ -34,17 +41,17 @@ GSDI can establish a taxonomic mapping between gene and species tree on the foll
   * taxonomic identifiers (e.g. "35932" from uniprot or ncbi)
   * taxonomy codes (e.g. "PYRHO") 
 
-=== 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"`
-  * 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"`.
 
 === 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 ==