Calibration File Format

The calibration file is used to provide divergence time calibration constraints to MEGA so that MEGA can convert relative divergence time estimates into absolute divergence times while respecting the given constraints.

There are three valid formats for providing calibration values in this file:

!NodeName=’some name’ minTime=1.75 maxTime=2.25

          With this format, the NodeName value must match an internal node label in the Newick file being evaluated.

!MRCA=’some name’ TaxonA='taxon A name' TaxonB='taxon B name' minTime=1.75 maxTime=2.25

          The value for MRCA is an internal node label that will be assigned to the target node. If a label for that target node is also supplied in the input Newick file, the label in the Newick file will be ignored. The values for TaxonA and TaxonB specify two leaf nodes whose most recent common ancestor in the active phylogeny is the calibration target node.

!MRCA='demoLabel1' TaxonA=chimpanzee TaxonB=bonobo Distribution=normal mean=6.4 stddev=1.2
!NodeName='demoLabel2' Distribution=exponential time=8.2 decay=0.25
!MRCA='orangutan-sumatran' TaxonA=orangutan TaxonB=sumatran Distribution=uniform mintime=4 maxtime=6

!MRCA='orangutan-sumatran' TaxonA=orangutan TaxonB=sumatran Distribution=lognormal offset=7.0 mean=2.38 stddev=0.15

          The four examples above specify statistical distributions to be used as calibration densities (can be one of normal, lognormal, exponential, or uniform). When using this format, each calibration density will be transformed into a pair of discrete constraints such that the minimum bound is placed at 2.5% of the density age and the maximum bound at the 97.5% of the density age. For instances, a normal distribution with mean equal to 10 and stddev equal to 1 would result in a constrain with minTime=8.04 and maxTime=11.96

Note*** When specifying an exponential distribution, one can use the keywords offset and lambda in place of time and decay respectively.

A single fixed time may be provided and for the RTDT analysis, this format should be used. For example:

          !NodeName=’some name’ time=2007

Optionally, a calibration can be given a name as the last parameter (e.g. !MRCA…calibrationName=‘myCalib’). Multiple calibrations may be provided, in which case, MEGA will generate absolute divergence times for all branching points in the active phylogeny while respecting all of the provided constraints. Each calibration must be on a single line and only one calibration can be provided per line. Taxa names must match those in the input Newick file. If a taxon name contains whitespace, the name must be placed in single quotes. Single quotes are not allowed inside taxa names.

The following are examples of valid calibration constraints:

         !MRCA='ch-bo' TaxonA='chimpanzee' TaxonB='bonobo' MinTime=0.8 MaxTime=5.0;

         !NodeName='myNode' time=6.3 calibrationName=’myCalib’;

         !NodeName='gorilla_human' MinTime=3.7 calibrationName='gorilla human';

         !MRCA='orangutan sumatran' TaxonA='orangutan' TaxonB='sumatran' MaxTime=11.0;

         !MRCA='demoLabel1' TaxonA=chimpanzee TaxonB=bonobo Distribution=normal mean=6.4 stddev=1.2
         !NodeName='demoLabel2' Distribution=exponential time=8.2 decay=0.25;   
         !MRCA='orangutan-sumatran' TaxonA=orangutan TaxonB=sumatran Distribution=uniform mintime=4 maxtime=6;

         !MRCA='orangutan-sumatran' TaxonA=orangutan TaxonB=sumatran Distribution=lognormal offset=7.0 mean=2.38 stddev=0.15