* -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 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"`.