The Calibration Times Editor allows you to enter multiple divergence time calibration constraints which will be used in the Time Tree analysis.
When you select the Time Tree analysis, 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. Next, you will be asked whether you want to specify divergence time calibration constraints. If you select No, then the Analysis Preferences dialog will be displayed for you to modify analysis options and only relative times of divergence will be calculated. If you select Yes, then both the Calibration Times Editor and the Tree Explorer will be displayed and they can be used in tandem to specify constraints.
Specifying Constraints
To specify a calibration constraint using the Calibration Times Editor, first click the New button. 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. Then, you may provide a 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 MEGAs 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. Additionally, if you want to provide an exact divergence time, just set the min and max times to the same value. Finally, click the Save Changes button to save the calibration constraint. Note: if you see a * after any calibrations, that means you havent yet saved some changes you made to it. Be careful to not navigate away from a calibration before saving it, or your modifications will be lost (even if you still see the * after navigating away).
To specify a calibration constraint using the Tree Explorer, select an internal node in the tree which is displayed in the Tree Explorer. This will enable the Add Calibration action. Select Compute | Add Calibration from the main menu in Tree Explorer (or click the Add Calibration button; a clock with a green plus sign). When you launch this action, a new calibration constraint will be created in the Calibration Times 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, and they are all saved, you can launch the analysis by clicking the Compute button at the top right of the Calibration Times Editor. This will cause the Analysis Preferences dialog to be displayed from which you can modify analysis options (model, gap treatment, etc ).
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,