Calibration Dialog

The Calibration Editor allows you to define multiple divergence time calibration constraints which will be used for the RelTime analyses.

When you select a RelTime 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 The branching pattern of a tree is its 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 this option,  the Calibration 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 a constraint type (see overview) from the Calibration | Calibrate MRCA menu. This will create a new calibration constraint and a dialog asking for constraint parameters will be shown. After entering the constraint parameters, you specify a node A node in a phylogenetic tree represents a taxon, the external or terminal nodes represent the extant taxa and the internal nodes represent the ancestral taxa. for which the new calibration applies by selecting two taxa A taxon is the individual unit whose evolutionary relationship is being investigated. Depending on the study, “taxa” may refer to species, populations, individuals, or sequences within an individual. from the Taxon A and Taxon B dropdown lists whose most recent common ancestor (MRCA) is the 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. You can edit the selected constraint's values at any time by clicking the edit button that is next to the constraint value(s). 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).

To specify a calibration constraint using the tree display, select an internal node in the tree and then select a constraint type from the Calibration | Calibrate Selected Node 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 OK button. This will 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 hereCalibration_File_Format. When you export a set of calibration constraints, they are saved in a format that can be imported into the Calibration Editor and also be used by the command-line version of MEGA (MEGA-CC MEGA-CC is the compute core that is used by MEGA and is distributed as a command-line application that is useful for iterative and batch analysis. It can be obtained from www.megasoftware.net .MEGA_CC)Also, once a time tree analysis is complete,