ARCH: Algorithms for Reconstructing Cancer Histories

More coming soon!

Existing methods

Bulk sequencing data

• HATCHet: identify copy-number aberrations from one or more bulk tumor sequencing samples
• DeCiFer: cluster single-nucleotide somatic variants (SNVs) using the descendent cell fraction (DCF) statistic
• PASTRI: infer tumor phylogenies using SNVs via importance sampling
• CALDER: infer tumor phylogenies from longitudinal samples using SNVs
• MACHINA: infer parsimonious metastatic seeding patterns from multi-site tumor sequencing samples

Single-cell sequencing data

• CHISEL: identify copy-number aberrations from single-cell DNA sequencing data
• SCARLET: infer tumor phylogenies from single-cell sequencing data using a loss-supported evolutionary model