* -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)
+
* -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"`
+ * 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 bases 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"`.
+ * 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 gene_tree.xml tree_of_life.xml out.xml`
+`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 ==