TIM model implemented in PartitionFinder2

[zcalamari]

RAxML-NG has three versions of the TIM model available, with equal and unequal frequencies for each (the chart linked in their manual is below). Does one of these TIM models correspond to the TIM model in PartitionFinder?

Thanks for the help!

Model | Reference | d.f. | Base freq | Symmetries | code
TIM1 | Posada, 2003 | 3 | equal | AC=GT ; AT=CG ; AG ; CT | 012230
TIM1uf | Posada, 2003 | 6 | unequal | AC=GT ; AT=CG ; AG ; CT | 012230
TIM2 |   | 3 | equal | AC=AT ; CG=GT ; AG ; CT | 010232
TIM2uf |   | 6 | unequal | AC=AT ; CG=GT ; AG ; CT | 010232
TIM3 |   | 3 | equal | AC=CG ; AT=GT ; AG ; CT | 012032
TIM3uf |   | 6 | unequal | AC=CG ; AT=GT ; AG ; CT | 012032

[Rob Lanfear]

Hi There,

The full details of all the partition finder models can be found in the models.csv file in the partfinder folder. This file contains those same codes (e.g. 012230) as well as telling you whether the frequencies are equal or unequal.

Rob