- * 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 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".
+ * 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")
+
+