Table 3.

Methods to infer tumor clonal composition from bulk DNA sequencing data.

Name	Using SSM or CNV for phylogeny reconstruction	Joint Deconvolution and Phylogeny inference?	Reference
PhyloWGS	SSM and percomuted CNV mixing proportion estimates	Joint Inference	118
Canopy	Both	Joint Inference	119
SPRUCE	SSM and percomuted CNV mixing proportion estimates	Joint Inference	120
PASTRI	SSM only	Two step clustering and Phylogeny Inference	121
PyClone	SSM only, corrects VAFs for CNV, does not use in reconstruction explicitly	Clustering and Identifying clonal genotypes only	122
SciClone	SSM only	Clustering and Identifying clonal genotypes only	123
THetA2	CNV only	Clustering and Identifying clonal genotypes only	124