=== 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'
+ * 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'.
=== Example ===