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Fig. 1 | BMC Genomics

Fig. 1

From: Clonal reconstruction from time course genomic sequencing data

Fig. 1

A schematic illustration of the clonal structure in an evolving bacterial population and the time course clonal reconstruction problem. a Starting from a single founder clone (shown in black) at time t1, four mutations (shown in red, green, yellow and blue, respectively) occur at time point t2 to t5, respectively, resulting in four novel clones (denoted by their unique variants). b The clonal tree represents the evolutionary history of these clones, in which each node represents a clone including the founder clone as the root, and each edge represents the mutations that occur at specific time points. c The Muller plot shows the evolutionary dynamics with the novel clones along with their frequencies at each time point. d Metagenome sequencing conducted at different time point, from which the variant allele frequencies (VAF) matrix can be derived. e The VAF matrix can be viewed as the product of the clonal tree (T) and the clone frequencies (C), similar to the formulation in cancer genomics [16]. The goal of this work is to reconstruct the clonal tree (T) and the clone frequencies (C) from the observed VAF matrix

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