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brettc / partitionfinder

PartitionFinder discovers optimal partitioning schemes for DNA sequences.
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TIM model #137

Closed zcalamari closed 3 years ago

zcalamari commented 3 years ago

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

zcalamari commented 3 years ago

Didn't realize there was a google group for partitionfinder. I'll move this there!