BEAST 2 Help Me Choose

# BEAST 2 Help Me Choose GTR rate AT

## GTR rate AT

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

### value

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 AT. 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.

### estimate

Rate AT 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 AT to true is recommended.

### lower

Since rate AT 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.

### upper

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

## References

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.