BEAST 2 Help Me Choose

BEAST 2 Help Me Choose GTR rate GT

GTR rate GT

Substitution rate between G and T (default 1) in the GTR (Tavaré, 1986) nucleotide substitution model.


Since the transversion rates (A <=> C, A <=> T, C <=> G and G <=> T) tend to be smaller than transition rates (A <=> G and C <=> T), one expects a value smaller than 1 for rate GT. The default of 1 makes a good starting value if estimated. If not estimated, a value based on prior information can be used, but this would reduce the uncertainty in the analysis.


Rate GT can vary per dataset, so it is usually estimated. Note that at least one of the GTR rates needs to be fixed (i.e. not estimated), because estimating them all leads to unidentifiability due to BEAST normalising rates so that the average rate is 1. Fixing a transition rate (rate AG or rate CT) usually provides more numerical stability than fixing a transversion rate), so setting estimate for rate GT to true is recommended.


Since rate GT is a rate parameter, it should always be positive and have a lower bound of at least 0. This is only relevant if estimate is true and ignored otherwise.


An upper value for the rate GT parameter is usually not set, though rate GT is usually in the range of 0 to 1. This is only relevant if estimate is true and ignored otherwise.


Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on mathematics in the life sciences. 1986 Dec 31;17(2):57-86.

See also substitution models.

Bayesian evolutionary analysis by sampling trees

Disclaimer: The above is the opinion of the author RB. If you do not agree, or spot a mistake, contact the author, or discuss this in the issues area or raise a new issue. A link will be added from this page to make sure others can find it.

Served through Jekyll, customised theme based on the twentyfourteen wordpress theme.