typo
Transactions are now turned on by default in NJTREE
"gene_tree" instead of "protein_tree"
Revert "Use the gdb2stn mlss-tag that has been created by MakeSpeciesTree"

This reverts commit f8e714c31fe7de93d84c5c24d38f7e13de225a50.
Here is the correct way to get the species tree