Methods and system for evaluating prevalence of genomes in a source. Estimated proportion values for genomes in a first and second sample of the source, taken at different times, are optimised based on prevalence data of segments in the samples and the genomes. The method may involve evaluating change in prevalence of reference genomes in a source, including maximising a probability function, such as a Poisson distribution or a global probability function, and optimising proportion values. Estimated proportion values may be optimised iteratively using a Hessian matrix. Input data may further comprise prevalence of variants of the segments, with indels or substitutions, in the genomes. Segments that do not correlate with the genomes may be categorised as paired or not paired end reads, and used to refine proportion values. Samples may comprise DNA segments, converted into protein segments, and prevalence determined by comparison to a reference library.
Metagenomic analysis of samples