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I am interested in reconstructing cell lineages based on the sequences of randomly partitioning plasmids.

I can find lots of models to build lineages based on a single sequence (e.g. bacterial gene) that is transmitted to all the offspring (in which case the signal comes only from substitutions in the sequence). But when working with plasmids, I cannot find any model that takes into account:

  • The independent mutations in some of the plasmids within the cell
  • The random partitioning (binomial segregation) of the wild and mutant plasmids

Essentially, I am looking for a metric to pair cells two by two based on the sequences of N plasmids per cell, and reconstruct the likely plasmid composition of their shared ancestor.

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