Table 1.
Clonal reconstruction methods based on SNV bulk data. Abbreviations: EM, expectation maximisation; MCMC, Markov chain Monte Carlo; MILP, mixed integer linear programming; QIP, quadratic integer programming.
| Software | Year | Reference | Phylogeny | Multiple samples | Inference |
|---|---|---|---|---|---|
| TrAp | 2013 | [37] | Y | N | Exhaustive search |
| Clomial | 2014 | [31] | N | Y | Binomial/EM |
| PhyloSub | 2014 | [32] | Y | Y | Tree-structured stick-breaking/MCMC |
| PyClone | 2014 | [38] | N | Y | Dirichlet process, beta-binomial/MCMC |
| RecBTP | 2014 | [39] | Y | N | Approximation algorithm |
| SciClone | 2014 | [40] | N | N | Beta mixture model |
| AncesTree | 2015 | [41] | Y | Y | Optimisation/MILP |
| CITUP | 2015 | [42] | Y | Y | Optimisation/QIP |
| LICHeE | 2015 | [43] | Y | Y | Heuristic |
| BayClone | 2015 | [44] | N | Y | Gibbs sampling/Metropolis-Hastings |
| CTPsingle | 2016 | [45] | Y | N | Dirichlet process, beta-binomial/MCMC |
| Cloe | 2016 | [46] | Y | Y | Metropolis-coupled MCMC |