The Calibration Editor allows you to enter multiple divergence time calibration constraints which will be used in the Timetree analysis.
When you select the Timetree analysis, the Timetree Wizard will be displayed and you will first be prompted to provide an alignment file (if one is not already activated) and a tree file which gives the topology for the time tree, and then specify an outgroup in the tree to place the root on. Next, you will have the option to specify divergence time calibration constraints. If you select Yes, then the Calibration Times Editor will be displayed and it can be used in specify divergence time calibration constraints.
Specifying Constraints
To specify a calibration constraint using the Calibration Editor, select Calibration | Calibrate MRCA. This will create a new calibration constraint with a default name. To specify a node for which the new calibration applies, select two taxa from the Taxon A and Taxon B dropdown lists whose most recent common ancestor (MRCA) is node to apply the constraint to. Next, edit the calibration name if the default name is not satisfactory. You may also edit the node label name (optional) in the MRCA Node Label edit box. This node label is useful for interpreting the tabular Time Tree output produced by MEGA’s Time Tree system so that you can quickly identify calibrated nodes by name instead of node number. Next, provide numerical values for the calibration constraints. You can provide min and max times, just a min time, or just a max time (as long as at least one min time and one max time are provided among all constraints). Additionally, if you want to provide an exact divergence time, just set the min and max times to the same value.
To specify a calibration constraint using the tree display, select an internal node in the tree and then select Calibration | Calibrate Selected Node from the main menu. When you launch this action, a new calibration constraint will be created in the Calibration Editor with two taxa already selected from the Taxon A and Taxon B dropdown lists. Then you can finish providing calibration parameters as described above.
Once you are finished specifying constraints, you can save your changes by clicking the Finished button. This will cause advance the Timetree Wizard to the next step.
Importing and Exporting
Calibration constraints can be imported from a text file or saved to a text file using the Import and Export features. Calibration constraints imported from text files must be formatted according to a set of rules which are described here. When you export a set of calibration constraints, they are saved in a format that can be imported into the Calibration Times Editor and also be used by the command-line version of MEGA (MEGA-CC)Also, once a time tree analysis is complete,