Table 1 Software tools for characterizing within-patient and intra-tumor heterogeneity and their features, including whether they capture SNVs, CNAs and structural variants (SVs), whether they support multiple biopsy analysis, and their key models and algorithms.

Software	Year	SNV	CNA	SV	Multiple	Model/Algorithm
OncoSNP¹⁷	2010		✓			Mixture model, EM, Bayesian methods
TuMult¹⁸	2010		✓		✓	Breakpoint distance
GRAFT¹⁹	2012		✓			Partial maximum likelihood
ABSOLUTE²⁰	2012	✓	✓			Maximum likelihood
TrAp²¹	2013	✓				Exhaustive search under constraints
THetA^22,23	2013		✓			Maximum likelihood
CancerTiming²⁴	2013		✓			Maximum likelihood
OncoSNP-seq²⁵	2013		✓			Mixture model, EM, Bayesian methods
PyClone²⁶	2014	✓			✓	Dirichlet Process, beta-binomial/MCMC
SciClone²⁷	2014	✓			✓	Beta mixture model/variational Bayes
Clomial²⁸	2014	✓			✓	Binomial mixture model, EM
CloneHD²⁹	2014	✓	✓		✓	HMM, EM, variational Bayes
MEDICC³⁰	2014		✓		✓	Finite state transducer, minimum-event distance
TITAN⁹	2014		✓			Two-chain factorial HMM/EM
SubcloneSeeker³¹	2014	✓	✓	✓		Clustering, enumeration and co-localization prediction
BTP³²	2014	✓				Binary tree partition
BreakDown³³	2014			✓		Maximum likelihood
PhyloSub³⁴	2014	✓			✓	Tree-structured stick-breaking process prior, MCMC
BayClone³⁵	2015	✓			✓	Categorical Indian Buffet Process
PhyloWGS⁵	2015	✓	✓		✓	Tree-structured stick-breaking process prior, MCMC
CITUP³⁶	2015	✓			✓	Quadratic integer programming
LICHeE³⁷	2015	✓			✓	Clustering and evolutionary constraint network
AncesTree³⁸	2015	✓			✓	Integer linear programming
SPRUCE⁶	2016	✓	✓		✓	Combinatorial enumeration
Canopy⁷	2016	✓	✓		✓	MCMC
THEMIS (our work)	2017	✓	✓		✓	Dynamic graphical models

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