# Single calibration point: Baltic Sea 0.01 mya (10 kya)
ruby snapp_prep.rb \
-p 39IDs.phy \
-t Species_39IDs.txt \
-s starting_tree_39IDs.newick \
-c Con_39IDs_Baltic_001mya.txt \
-x 39IDs_SNAPP_calib_only_Baltic_001mya.xml


# Single root calibration point: 0.68 mya
ruby snapp_prep.rb \
-p 39IDs.phy \
-t Species_39IDs.txt \
-s starting_tree_39IDs.newick \
-c Con_39IDs_root_068mya.txt \
-x 39IDs_SNAPP_calib_root_068mya.xml



# Single root calibration point: 1 mya
ruby snapp_prep.rb \
-p 39IDs.phy \
-t Species_39IDs.txt \
-s starting_tree_39IDs.newick \
-c Con_39IDs_root_1mya.txt \
-x 39IDs_SNAPP_calib_root_1mya.xml


# Single root calibration point — 2 mya
ruby snapp_prep.rb \
-p 39IDs.phy \
-t Species_39IDs.txt \
-s starting_tree_39IDs.newick \
-c Con_39IDs_root_2mya.txt \
-x 39IDs_SNAPP_calib_root_2mya.xml



# Calibration points: Baltic + root 068 mya
ruby snapp_prep.rb \
-p 39IDs.phy \
-t Species_39IDs.txt \
-s starting_tree_39IDs.newick \
-c Con_39IDs_001_plus_068mya.txt \
-x 39IDs_SNAPP_calib_Baltic_root_068mya.xml


# Calibration points: Baltic + root 1 mya
ruby snapp_prep.rb \
-p 39IDs.phy \
-t Species_39IDs.txt \
-s starting_tree_39IDs.newick \
-c Con_39IDs_001_plus_1mya.txt \
-x 39IDs_SNAPP_calib_Baltic_root_1mya.xml



# Calibration points: Baltic + root 2 mya
ruby snapp_prep.rb \
-p 39IDs.phy \
-t Species_39IDs.txt \
-s starting_tree_39IDs.newick \
-c Con_39IDs_001_plus_2mya.txt \
-x 39IDs_SNAPP_calib_Baltic_root_2mya.xml
