Table 1.

Nine clone prediction methods tested

Method	Considers CNAs	Phylogeny produced	Clone count estimated	Multiple solutions	Reference
AncesTree	NO	YES	YES	NO	El-Kebir et al. (2015)
BayClone2	YES	NO	NO	NO	Sengupta et al. (2015)
Canopy	YES	YES	NO	NO	Jiang et al. (2016)
CITUP	NO	YES	YES	YES	Malikic et al. (2015)
Clomial	NO	NO	NO	NO	Zare et al. (2014)
CloneFinder	NO	YES	YES	NO	Miura et al. (in this article)
cloneHD	YES	NO	YES	NO	Fischer et al. (2014)
LICHeE	NO	YES	YES	NO	Popic et al. (2015)
PhyloWGS	YES	YES	YES	YES	Deshwar et al. (2015)

CNAs, copy number alterations.