| boundsGamma | Upper limit for overall mutation rate |
| distLRR | Find summary statistics of LRR |
| expectedMutationRate | Expected mutation rate of a mutation matrix |
| findReversible | Find reversible mutation matrix |
| fratio | Calculates fratio |
| lik2 | Pairwise likelihood with mutation |
| mut2 | mut2: Transforming mutation models to reversibility |
| mut2-package | mut2: Mutation stuff |
| simLRR | Simulate LRR |
| snpExample | SNP example |
| tabfRatio | Produce table comparing transformations |
| tabLRR | Produce table comparing transformations based on simulations |
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