Code accompanying this paper - 'A scalable method for identifying frequent subtrees in sets of large phylogenetic trees - Avinash Ramu, Tamer Kahveci and J Gordon Burleigh.'
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DeNovoGear with BetaBinomial likelihoods for paired sample mutation calling. For example this package can be used to do tumor vs normal comparisons. The BetaBinomial likelihood model has been shown to have a higher sensitivity and specificity compared to the binomial model.
denovogear-VNTR-code
denovo caller using beta binomial likelihoods
Public repository.