Table 1 Subclonal reconstruction methods, their properties and assumptions
From: PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors
Property/method | PhyloWGS | PhyloSub [ 17 ] | THetA [ 15 ] | PyClone [ 18 ] | TrAp [ 16 ] | Clomial [ 36 ] | RecBTP [ 33 ] |
|---|---|---|---|---|---|---|---|
Simple somatic mutation | Y | Y | N | Y | Y | Y | Y |
Copy number variation | Y | N | Y | N | N | N | N |
Weak parsimony | Y | Y | N/A | Y | Y | Y | Y |
Strong parsimony | N | N | N/A | N | Y | N | Y |
Infinite sites | Y | Y | N/A | Y | Y | N | Y |
Phylogenetic inference | Y | Y | N | N | Y | N | Y |
Parametric | N | N | Y | N | N | Y | N |
Multiple samples | Y | Y | N | Y | N | Y | N |
Genotype uncertainty | Y | Y | N | N/A | N | N | N |