Fig. 2.

Schematic of the Concerti Framework. Given a set of multi-patient (COVID-19) or multi-site, multi-time (cancer) genomic samples, the algorithm analyzes the underlying alteration frequency distribution as input and performs a (1) negative selection to filter appearing alterations. A (2) multidimensional clustering is done to identify pseudoclones/lineages that will then be enriched by a (3) single sample clustering that (4) merges alterations that were initially negatively selected. (5) All potential phylogenies are generated and assessed for compatibility according to Definition 1. Finally the set of consolidated phylogenetic structures over time or site are output with likelihood scores