BitPhylogeny: A Probabilistic Framework for Reconstructing Intra-tumor Phylogenies
summary
Probabilistic pipeline reconstructs intra-tumor phylogenies from phased reads using a tree-structured Dirichlet process prior that yields node masses summing to 1, a transition kernel encoding methylation or infinite-sites mutation models, and a tailored MCMC sampler. Applied to bisulfite sequencing of a 201 bp locus with 8 CpGs across multi-region samples it separates left/right topologies; applied to 56 single cells with ~700 SNVs it recovers a 41-cell monoclonal arm plus early branching. MCMC is slow and tree-comparison remains an open problem.
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