Software

ΛΑΞΣΕΙΣ is an R package to infer tumor evolution during malignant transformation from bulk whole genome sequencing data. It uses somatic variants as a molecular clock to date malignant transformation (in the tumor's most recent common ancestor, MRCA) and the acquisition of clonal copy number changes. Additionally, ΛΑΞΣΕΙΣ tests whether there is evidence for an early common ancestor (ECA), oncogenic events acquired prior to malignant transformation. ΛΑΞΣΕΙΣ also provides modalities to compare tumor evolution across patient collectives, and to correlate evolutionary timings with outcome.

SCIFER is an R package to quantify selection and drift from the somatic variant allele frequency distribution measured with single-time point bulk whole genome sequencing. SCIFER provides functions to compute the expected variant allele frequency distribution in somatic tissues that are either expanding or homeostatic. Modalities for both, neutrally evolving tissues and tissues with selection of a single or multiple clone are provided. The computations assume deterministic cell numbers in the tissue overall but account for the stochasticity of clonal growth at the level of individual clones, using clone size distributions generated by linear birth-death processes.