Table 2.
Clonal reconstruction methods based on SNV and CNA bulk data. Abbreviations: HMM, hidden Markov model; MCMC, Markov chain Monte Carlo.
| Software | Year | Reference | Phylogeny | Multiple samples | Inference |
|---|---|---|---|---|---|
| CHAT | 2014 | [54] | N | N | Dirichlet process Gaussian mixture model/MCMC |
| CloneHD | 2014 | [55] | N | Y | HMM/local optimisation |
| SubcloneSeeker | 2014 | [56] | Y | Y | Exhaustive enumeration |
| PhyloWGS | 2015 | [58] | Y | Y | Tree-structured stick-breaking/MCMC |
| SCHISM | 2015 | [57] | Y | Y | Likelihood ratio tests/genetic algorithm |
| SPRUCE | 2016 | [59] | Y | Y | Exhaustive enumeration |
| CANOPY | 2016 | [60] | Y | Y | MCMC |