Table 1 Exemplar phylogenetic methods
Method | Input data | Data mode | CNV | Multi-time data | Multi-site data | Multi-patient data | Genomic scale | Time-scaled tree |
|---|---|---|---|---|---|---|---|---|
SCITE [13] | single cell | single value | ✗ | ✗ | ✗ | ✗ | N/A | ✗ |
Pyclone [20] | bulk data | single value | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ |
CITUP [18] | bulk data | single value | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ |
Calder [25] | bulk data | single value | ✗ | ✓ | ✗ | ✗ | ✗ | ✓ |
VERSO [4] | bulk data | single value | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ |
BEAST [26] | bulk data | single value | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ |
ClonalTREE [27] | bulk data | single value | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
PhylogicNDT [24] | bulk data | dist. | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ |
Concerti | bulk data | dist. | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |